openapi: 3.0.3 info: title: Tamarind API description: | API for protein structure prediction, design, and analysis tools. ## Authentication All API endpoints require authentication via API key in the request headers: ``` Authorization: Bearer YOUR_API_KEY ``` ## Job Types The API supports various job types for different protein analysis tasks including: - Structure prediction (AlphaFold, Chai, Boltz, etc.) - Protein design (RFdiffusion, ProteinMPNN, etc.) - Docking (AutoDock Vina, DiffDock, etc.) - Property prediction (solubility, thermostability, etc.) - And many more specialized tools ## File Uploads Many tools require PDB files, sequences, or other molecular data. Use the `/uploadFile` endpoint to upload files and get file IDs for use in job submissions. ## Rate Limits - All endpoints: 10 requests per second version: 1.0.0 contact: name: Tamarind Support email: support@tamarind.com license: name: MIT url: https://opensource.org/licenses/MIT servers: - url: https://api.tamarind.com/v1 description: Production server - url: https://staging-api.tamarind.com/v1 description: Staging server paths: /submit-job: post: summary: Submit a single job description: Submit a job for protein analysis using one of the available tools operationId: submitJob security: - ApiKeyAuth: [] requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/JobSubmission' example: jobName: "my-protein-analysis" type: "alphafold" settings: sequence: "MKTVRQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPRGYVLAGG" responses: '200': description: Job submitted successfully content: application/json: schema: $ref: '#/components/schemas/JobResponse' '400': description: Bad request - invalid parameters content: application/json: schema: $ref: '#/components/schemas/ErrorResponse' '401': description: Unauthorized - invalid API key '429': description: Too many requests - rate limit exceeded tags: - Jobs /submit-batch: post: summary: Submit multiple jobs as a batch description: Submit multiple jobs in a single request for batch processing operationId: submitBatch security: - ApiKeyAuth: [] requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/BatchSubmission' example: batchName: "my-batch-analysis" type: "alphafold" settings: - sequence: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" - sequence: "MKTVRQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPRGYVLAGG" jobNames: - "job1" - "job2" responses: '200': description: Batch submitted successfully content: application/json: schema: $ref: '#/components/schemas/BatchResponse' '400': description: Bad request - invalid parameters '401': description: Unauthorized '429': description: Too many requests tags: - Jobs /jobs: get: summary: Get user's jobs description: Retrieve a list of jobs for the authenticated user operationId: getJobs security: - ApiKeyAuth: [] parameters: - name: jobName in: query description: Return one job given its name schema: type: string example: "myJobName" - name: batch in: query description: Return all jobs in a batch schema: type: string example: "myBatchName" - name: startKey in: query description: Use a previously returned start key to retrieve more than 1000 jobs schema: type: string - name: limit in: query description: Limit the number of jobs retrieved, if there are additional jobs a startKey will be returned schema: type: integer default: 1000 - name: organization in: query description: Return all jobs in your organization schema: type: string enum: ["true"] - name: includeSubjobs in: query description: Include subjobs from batches in response - only top level jobs are returned by default schema: type: string enum: ["true"] - name: jobEmail in: query description: Return jobs for another member in your organization schema: type: string format: email example: "user@email.com" responses: '200': description: List of jobs content: application/json: schema: oneOf: - type: object properties: jobs: type: array items: $ref: '#/components/schemas/JobInfo' startKey: type: string description: Key for pagination to retrieve more jobs statuses: type: object properties: Complete: type: integer description: Number of completed jobs "In Queue": type: integer description: Number of jobs in queue Running: type: integer description: Number of running jobs Stopped: type: integer description: Number of stopped jobs - $ref: '#/components/schemas/JobInfo' description: Single job response when jobName parameter is used '401': description: Unauthorized tags: - Jobs /result: post: summary: Get job results description: Retrieve results for a completed job operationId: getResult security: - ApiKeyAuth: [] requestBody: required: true content: application/json: schema: type: object required: - jobName properties: jobName: type: string description: Name of the job to get results for example: "my-protein-analysis" jobEmail: type: string format: email description: Email of another member of your team (optional) example: "user@email.com" fileName: type: string description: Path to a specific file in the job results (optional) example: "myfile.txt" pdbsOnly: type: boolean description: Return only PDB files (optional) example: true responses: '200': description: Job results content: application/json: schema: type: string description: S3 presigned URL to download the job results example: "https://s3.amazonaws.com/bucket/job-results.zip" '400': description: Bad request '401': description: Unauthorized '404': description: Job not found tags: - Results /upload/{filename}: put: summary: Upload a file description: Upload a file (PDB, sequence, etc.) for use in job submissions operationId: uploadFile security: - ApiKeyAuth: [] parameters: - name: filename in: path required: true description: Name of the file to upload schema: type: string example: "myfile.pdb" - name: folder in: query description: Optional folder to upload the file to schema: type: string example: "myFolder" requestBody: required: true content: application/octet-stream: schema: type: string format: binary description: File content to upload responses: '200': description: File uploaded successfully content: application/json: schema: type: object properties: message: type: string description: Success message example: "File uploaded successfully" fileUrl: type: string description: URL of the uploaded file signedUrl: type: string description: Signed URL for accessing the file '400': description: Bad request - invalid file '401': description: Unauthorized '413': description: File too large tags: - Files /delete-job: post: summary: Delete a job description: Delete a job given its name. If a job name is provided which does not exist, it returns a 400 error. If you delete a batch job, all subjobs will be deleted also. operationId: deleteJob security: - ApiKeyAuth: [] requestBody: required: true content: application/json: schema: type: object required: - jobName properties: jobName: type: string description: Name of the job to delete example: "myJobName" responses: '200': description: Job deleted successfully content: application/json: schema: type: object properties: message: type: string example: "Job deleted successfully" '400': description: Bad request - job not found '401': description: Unauthorized tags: - Jobs /delete-file: get: summary: Delete a file description: Delete a file from user account operationId: deleteFile security: - ApiKeyAuth: [] parameters: - name: filePath in: query description: Name of the file to delete schema: type: string example: "path/to/myFileName.txt" - name: folder in: query description: Path to folder - deletes all files in the specified folder schema: type: string example: "myFolder" responses: '200': description: File deleted successfully content: application/json: schema: type: object properties: message: type: string example: "File deleted successfully" '400': description: Bad request - file not found '401': description: Unauthorized tags: - Files /files: get: summary: Get user's files description: Retrieve a list of files uploaded by the user operationId: getFiles security: - ApiKeyAuth: [] parameters: - name: limit in: query description: Maximum number of files to return schema: type: integer default: 50 maximum: 100 - name: offset in: query description: Number of files to skip schema: type: integer default: 0 - name: includeFolders in: query description: Include folders in the response schema: type: string enum: ["true"] - name: folder in: query description: Path to folder to view files within that folder schema: type: string example: "myFolder" responses: '200': description: List of files content: application/json: schema: type: object properties: files: type: array items: type: object properties: fileId: type: string description: Unique identifier for the file fileName: type: string description: Original filename fileSize: type: integer description: File size in bytes uploadTime: type: string format: date-time description: When the file was uploaded total: type: integer description: Total number of files hasMore: type: boolean description: Whether there are more files available '401': description: Unauthorized tags: - Files components: securitySchemes: ApiKeyAuth: type: apiKey in: header name: x-api-key description: API key for authentication schemas: # Tool schemas ref # Abb4 Settings Abb4Settings: type: object required: - heavy - light - numSamples properties: heavy: type: string description: "Antibody heavy chain variable region sequence" example: "QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSLAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARGGSVSGTLVDFDIWGQGTMVTVS" light: type: string description: "Antibody light chain variable region sequence" example: "DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNIYPITFGGGTKVEIK" numSamples: type: number description: "Number of conformational samples to generate per input sequence" minimum: 1 maximum: 1000 default: 100 model: type: string description: "Checkpoint to use for inference" default: "abb4_STEROIDS" enum: - "abb4_STEROIDS" - "abb4_STEROIDS_CG" - "abb4_base" numTimesteps: type: number description: "Number of ODE steps during inference. 100 matches publication; 50 is ~identical with a 2x speedup; 10-20 is faster with some accuracy drop" minimum: 5 maximum: 200 default: 50 renumber: type: boolean description: "Post-process predicted PDBs to use standard IMGT antibody numbering" default: True # Abgpt Settings AbgptSettings: type: object required: - startingResidues - chainType properties: startingResidues: type: string description: "Starting sequence for your generated BCR" example: "QVQL" chainType: type: string description: "Heavy or light chain" default: "heavy" enum: - "heavy" - "light" numSequences: type: number description: "Number of sequences to generate" default: 100 # Ablang Settings AblangSettings: type: object required: - task - heavyMask - lightMask properties: task: type: string default: "scan" enum: - "scan" - "embeddings" - "mask" heavySequence: type: string description: "Heavy sequence of your antibody" example: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" lightSequence: type: string description: "Light sequence of your antibody" example: "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIN" heavyMask: type: string description: "Residues to mask in the heavy chain, masking the whole sequence is not allowed [Only available when task is one of mask]" example: "26-32" lightMask: type: string description: "Residues to mask in the light chain, masking the whole sequence is not allowed [Only available when task is one of mask]" example: "26-32" # Ablang-Mpnn Settings AblangMpnnSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure in PDB format File with extensions [pdb]" example: "3HTN.pdb" format: binary heavyChain: type: string description: "Chain identifier for heavy chain" customHeavyResidues: type: string description: "Select specific residues to design on heavy chain" lightChain: type: string description: "Chain identifier for light chain" example: "L" customLightResidues: type: string description: "Select specific residues to design on light chain" mpnn_weight: type: number description: "Weight for ProteinMPNN model in ensemble (0-1)" minimum: 0 maximum: 1 default: 0.5 ablang_weight: type: number description: "Weight for AbLang model in ensemble (0-1)" minimum: 0 maximum: 1 default: 0.5 temperature: type: number description: "Sampling temperature for sequence generation" minimum: 0.01 maximum: 2 default: 0.1 num_sequences: type: number description: "Number of sequences to generate" minimum: 1 maximum: 100 default: 5 # Abmap Settings AbmapSettings: type: object required: - task - chainType properties: task: type: string default: "embeddings" enum: - "embeddings" sequence: type: string description: "Sequence to embed" example: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" chainType: type: string default: "H" enum: - "H" - "L" # Abmpnn Settings AbmpnnSettings: type: object required: - pdbFile - designedResidues - regions properties: pdbFile: type: string description: "Protein structure file to be designed File with extensions [pdb]" example: "9f6o.pdb" format: binary designedChains: type: array items: type: string description: "Chain IDs to be designed - choose heavy before light chain" example: ["B"] designedResidues: type: object description: "Residues to design in your protein" example: {'B': '26 27 28 29 30 31 32 52 53 54 55 56 95 96 97 98 99 100 101 102'} numSequences: type: number description: "Number of sequences to be generated for each protein backbone" default: 2 temperature: type: number description: "Model temperture - Suggested values 0.1, 0.15, 0.2, 0.25, 0.3. Higher values will lead to more diversity" minimum: 0 maximum: 1 default: 0.1 noiseLevel: type: string description: "Select from models of various noise levels (A)" default: "0.2" enum: - "0.02" - "0.1" - "0.2" - "0.3" omitAAs: type: string description: "These amino acids will be avoided when generating sequences" default: "C" verifySequences: type: string description: "Automatically perform structure prediction on generated sequences for verification" enum: - "verify-alphafold" - "verify-chai" detectCDRs: type: boolean description: "Must input chains as format 'H L' to detect CDRs" default: False regions: type: string description: "Regions to mutate" example: ["CDRH1", "CDRH2", "CDRH3"] enum: - "FWH1" - "FWL1" - "CDRH1" - "CDRL1" - "FWH2" - "FWL2" - "CDRH2" - "CDRL2" - "FWH3" - "FWL3" - "CDRH3" - "CDRL3" - "FWH4" - "FWL4" # Abnativ Settings AbnativSettings: type: object required: - task - sequence - nat - vhSequence - vlSequence properties: task: type: string default: "score" enum: - "score" - "paired_score" - "hum_vhh" - "hum_vh_vl" - "hum_vh_vl_paired" sequence: type: string description: "Sequence [Only available when task is one of score, hum_vhh]" example: "QVQLVESGGGLVQAGGSLRLSCAASGRTFSSYAMGWFRQAPGKEREFVAAISWSGGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADSTIYASYYECGHGLSTGGYGYDSWGQGTQVTVSS" maxLength: 5000 nat: type: string example: "VHH2" default: "VHH2" enum: - "VH2" - "VL2" - "VHH2" vhSequence: type: string description: "VH Sequence [Only available when task is one of paired_score, hum_vh_vl, hum_vh_vl_paired]" example: "EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS" maxLength: 5000 vlSequence: type: string description: "VL Sequence [Only available when task is one of paired_score, hum_vh_vl, hum_vh_vl_paired]" example: "DIQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKRLIYAASSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCLQHNSYPLTFGGGTKVEIK" maxLength: 5000 # Abodybuilder Settings AbodybuilderSettings: type: object required: - heavy - light properties: heavy: type: string description: "Antibody heavy chain sequence" example: "QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSLAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARGGSVSGTLVDFDIWGQGTMVTVS" light: type: string description: "Antibody light chain sequence" example: "DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNIYPITFGGGTKVEIK" # Adapt Settings AdaptSettings: type: object required: - pmhcTargets - tcrPdbids - designCdrs - numDesigns properties: pmhcTargets: type: string description: "TSV file with columns: organism, mhc_class, mhc, peptide. Example: human, 1, A*02:01, GILGFVFTL File with extensions [tsv]" example: "example_pmhc_targets_adapt.tsv" format: binary tcrPdbids: type: string description: "Space-separated PDB IDs to use as TCR templates" example: "1oga 5bs0 3gsn 3qdg" default: "1oga 5bs0 3gsn 3qdg" designCdrs: type: string description: "Space-separated CDR indices (0=CDR1A, 1=CDR2A, 2=CDR2.5A, 3=CDR3A, 4=CDR1B, 5=CDR2B, 6=CDR2.5B, 7=CDR3B)" example: "0 1 3 4 5 7" default: "0 1 3 4 5 7" numDesigns: type: number description: "Number of TCR design iterations to perform" minimum: 1 maximum: 100 default: 10 # Admet Settings AdmetSettings: type: object required: - smilesStrings properties: smilesStrings: type: string description: "List of SMILES strings to predict properties for" example: ["C1=C(C)C=CC=C1", "CC(=O)OC1=CC=CC=C1C(=O)O"] default: [] # Aev-Plig Settings AevPligSettings: type: object required: - pdbFile - sdfFile properties: pdbFile: type: string description: "PDB file containing the protein structure File with extensions [pdb]" example: "1a30.pdb" format: binary sdfFile: type: string description: "SDF file containing the bound ligand 3D structure File with extensions [sdf]" example: "1a30.sdf" format: binary # Af-Multistate Settings AfMultistateSettings: type: object required: - sequence properties: sequence: type: string description: "GPCR protein sequence" example: "MEDFNMESDSFEDFWKGEDLSNYSYSSTLPPFLLDAAPCEPESLEINKYFVVIIYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALADLLFALTLPIWAASKVNGWIFGTFLCKVVSLLKEVNFYSGILLLACISVDRYLAIVHATRTLTQKRYLVKFICLSIWGLSLLLALPVLLFRRTVYSSNVSPACYEDMGNNTANWRMLLRILPQSFGFIVPLLIMLFCYGFTLRTLFKAHMGQKHRAMRVIFAVVLIFLLCWLPYNLVLLADTLMRTQVIQETCERRNHIDRALDATEILGILHSCLNPLIYAFIGQKFRHGLLKILAIHGLISKDSLPKDSRPSFVGSSSGHTSTTL" state: type: string description: "State to model GPCR in" default: "active" enum: - "active" - "inactive" # Af-Traj Settings AfTrajSettings: type: object required: - sequence properties: sequence: type: string description: "Amino acid sequence" example: "KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEG" # Af-Unmasked Settings AfUnmaskedSettings: type: object required: - sequence - templateFile properties: sequence: type: string description: "Protein amino acid sequence, use : to separate chains for multimers" maxLength: 5000 templateFile: type: string description: "Experimental structure to use as template. Note: must have same number of chains as target sequence. File with extensions [pdb]" format: binary modelType: type: string description: "AlphaFold multimer model version (v2 or v3)" default: "multimer_v3" enum: - "multimer_v2" - "multimer_v3" predictionsPerModel: type: number description: "Number of predictions to generate per model" minimum: 1 maximum: 50 default: 5 useDropout: type: boolean description: "Whether to use dropout during inference for stochastic predictions" default: False modelsToUse: type: string description: "Comma-separated list of models to run (e.g., 'model_5_multimer_v3' or 'model_5_multimer_v3,model_1_multimer_v3'). Model 5 is best. Leave empty to run all 5 models. Running fewer models = ~5x faster." crossChainTemplatesOnly: type: boolean description: "Use only inter-chain template constraints, skipping intra-chain templates for moderate speedup" default: False inpaint_clashes: type: boolean description: "Automatically detect and delete clashing sets of amino acids between templates" default: True align: type: boolean default: False repeat_template: type: number description: "Number of times the template is added as an Alphafold input" minimum: 1 maximum: 4 default: 4 # Af2Bind Settings Af2bindSettings: type: object required: - pdbFile - chain properties: pdbFile: type: string description: "pdb structure to find binding pocket File with extensions [pdb]" example: "insulin_target.pdb" format: binary chain: type: string description: "Chain to predict" example: "A" # Af2Rave Settings Af2raveSettings: type: object required: - sequence properties: sequence: type: string description: "Sequence of the protein to design and sample" example: "MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKE" # Afcluster Settings AfclusterSettings: type: object required: - a3mFile properties: a3mFile: type: string description: "a3m file with MSA results to be clustered File with extensions [a3m]" format: binary # Afcycdesign Settings AfcycdesignSettings: type: object required: - pdbFile - chain properties: pdbFile: type: string example: "7m28.pdb" format: binary chain: type: string example: "A" numDesigns: type: integer default: 1 # Afsample Settings AfsampleSettings: type: object required: - sequence properties: sequence: type: string description: "Protein amino acid sequence, use : to separate chains for multimers" example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" # Aggrescan3D Settings Aggrescan3dSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Pdb structure file of the protein or protein complex File with extensions [pdb]" example: "9f6o.pdb" format: binary # Alde Settings AldeSettings: type: object required: - csvFile properties: csvFile: type: string description: "CSV with training data File with extensions [csv]" format: binary # Align-Pdbs Settings AlignPdbsSettings: type: object required: - pdbFiles properties: pdbFiles: type: string description: "PDB files to align File with extensions [pdb]" example: ["1a3n.pdb", "PDB2.pdb"] format: binary alignChain: type: string description: "Chain to align on" # Allmetal3D Settings Allmetal3dSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure in pdb format to add waters to File with extensions [pdb]" example: "1iep.pdb" format: binary models: type: string description: "Model to use" default: "all" enum: - "all" - "water3d" - "allmetal3d" mode: type: string description: "Prediction mode to use" default: "fast" enum: - "fast" - "all" - "site" centralResidue: type: string radius: type: number threshold: type: number # Alphabind-Finetune Settings AlphabindFinetuneSettings: type: object required: - csvFile - sequenceColumn - targetColumn - KdColumn properties: csvFile: type: string description: "CSV file containing your sequences and property of interest File with extensions [csv]" format: binary sequenceColumn: type: string description: "Title of the column containing the sequences of the binders to be modified" targetColumn: type: string description: "Title of the column containing the sequences of the binders to be modified" KdColumn: type: string description: "Title column containing binding affinity number" # Alphacutter Settings AlphacutterSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure file in PDB format to be processed by AlphaCutter. File with extensions [pdb]" example: "1a3n.pdb" format: binary loop_min: type: number description: "Minimum loop length to be considered as non-globular region. Decrease to remove shorter loops." example: "20" minimum: 0 default: 20 helix_min: type: number description: "Minimum helix length to be considered as non-globular region. Decrease to remove shorter helices." example: "30" minimum: 0 default: 30 fragment_min: type: number description: "Minimum domain fragment length to be considered a domain region. Increase to exclude larger fragments." example: "5" minimum: 0 default: 5 domain_min: type: number description: "Minimum domain length to be output as a domain. Increase to exclude larger domains." example: "0" minimum: 0 default: 0 pLDDT_min: type: number description: "Minimum average pLDDT score of domain residues to be output. Excludes domains with low pLDDT." example: "70.0" minimum: 0 maximum: 100 default: 0 local_contact_range: type: number description: "Defines distance cutoff distinguishing local from non-local contacts used in domain identification." example: "5" minimum: 0 default: 5 domain_out: type: boolean description: "If true, outputs every non-contacting domain as a separate PDB file." default: False single_out: type: boolean description: "If true, outputs all domains merged into a single PDB file." default: False # Alphaflow Settings AlphaflowSettings: type: object required: - task - sequence - conformations properties: task: type: string default: "alphaflow" enum: - "alphaflow" - "esmflow" sequence: type: string example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" model: type: string description: "Model to use for prediction" default: "pdb" enum: - "pdb" - "md-atlas" conformations: type: number default: 10 msaFile: type: string description: "Multiple sequence alignment file in a3m format File with extensions [a3m] [Only available when task is one of alphaflow]" format: binary numBatches: type: integer description: "Will submit multiple parallel batches each with your selected number of conformations" maximum: 100 default: 1 # Alphafold Settings AlphafoldSettings: type: object required: - sequence properties: sequence: type: string description: "Protein amino acid sequence, use : to separate chains for multimers" example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" maxLength: 5000 numModels: type: string description: "Number of models to be used, each generating a different prediction" default: "5" enum: - "1" - "2" - "3" - "4" - "5" numRecycles: type: number description: "Number of times to recycle outputs back through structure prediction process for refined results" minimum: 0 maximum: 20 default: "3" numRelax: type: number description: "Number of models to perform amber relaxation for more accurate side chain predictions" minimum: 0 maximum: 5 default: 0 useMSA: type: boolean description: "When MSAs are disabled, AlphaFold will run in single sequence mode." default: True pairMode: type: string description: "\"unpaired_paired\" = pair sequences from same species + unpaired MSA, \"unpaired\" = seperate MSA for each chain, \"paired\" - only use paired sequences." example: "unpaired_paired" enum: - "paired" - "unpaired" - "unpaired_paired" msaDatabase: type: string description: "Select how the MSA is generated using UniRef30, SwissProt, and the ColabFold environmental database." example: "uniref" default: "uniref" enum: - "uniref" - "swissprot" - "uniref+swissprot" templateMode: type: string description: "Choose which template mode to use for your prediction" default: "pdb100" enum: - "pdb100" - "custom" - "none" templateFiles: type: string description: "Use custom structural templates in your prediction File with extensions [cif]" format: binary logan: type: boolean description: "Use BFVD Logan MSA for prediction" bfvdTemplates: type: boolean description: "Query BFVD for template structures to use for your prediction" default: False randomSeed: type: number description: "Random seed to be used in structure prediction" maxMsa: type: string description: "Max # Clusters : Max # Extra Sequences - decrease max_msa to increase uncertainity" example: "508:2048" enum: - "508:2048" - "512:1024" - "256:512" - "128:256" - "64:128" - "32:64" - "16:32" recycleEarlyStopTolerance: type: string description: "Run recycles until distance between recycles is within a given tolerance (0 = never stop early)" enum: - "0.0" - "0.5" - "1.0" ipsaeScoring: type: boolean description: "Use IPSAE scoring function for interprotein interactions" default: False dropout: type: boolean default: False modelType: type: string description: "Model type to be used. If auto selected, will use alphafold2_ptm for monomer prediction and alphafold2_multimer_v3 for complex prediction (recommended canonical weights). Any of the mode_types can be used (regardless if input is monomer or complex)" default: "auto" enum: - "auto" - "alphafold2_ptm" - "alphafold2_multimer_v1" - "alphafold2_multimer_v2" - "alphafold2_multimer_v3" - "deepfold_v1" - "alphafold2" chooseBest: type: boolean description: "Return only the best confidence model (rank_001) or all generated models" default: True # Amplify Settings AmplifySettings: type: object required: - sequence properties: sequence: type: string example: "EVQLVQSGPEVKKPGTSVKVSCKASGFTFMSSAVQWVRQARGQRLEWIGWIVIGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSSISCNDGFDIWGQGTMVTVS" # Anarci Settings AnarciSettings: type: object required: - sequence properties: sequence: type: string example: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" scheme: type: string default: "kabat" enum: - "imgt" - "kabat" - "chothia" - "martin" - "aho" - "wolfguy" # Ancestral-Reconstruction Settings AncestralReconstructionSettings: type: object required: - alignmentFile properties: alignmentFile: type: string description: "FASTA file with sequences (minimum 3 sequences). Unaligned sequences will be automatically aligned with MAFFT. File with extensions [fasta, fa, aln, phy, phylip]" example: "cytochrome_c_aligned.fasta" format: binary mode: type: string description: "AA (protein), DNA (nucleotide), CODON (codon-aware, slower)." default: "AA" enum: - "AA" - "DNA" - "CODON" outgroup: type: string description: "Sequence ID to root the tree. Must match a sequence name exactly." example: "frog_GAPDH" model: type: string description: "MFP auto-selects. JTT/WAG/LG/Dayhoff for proteins; GTR/HKY/JC/K2P for DNA." default: "MFP" enum: - "MFP" - "JTT" - "WAG" - "LG" - "Dayhoff" - "GTR" - "HKY" - "JC" - "K2P" bootstrap: type: number description: "Replicates for branch support. 1000+ recommended for publication-quality results." minimum: 100 maximum: 10000 default: "1000" fast: type: boolean description: "Enable fast tree search (faster, less thorough)." default: False # Antiberty Settings AntibertySettings: type: object required: - task - heavyChain - heavyMask - lightChain - lightMask properties: task: type: string default: "antibody-mask" enum: - "antibody-mask" - "nanobody-mask" - "antibody-log-likelihood" - "nanobody-log-likelihood" - "antibody-embeddings" - "nanobody-embeddings" heavyChain: type: string example: "EVQLVQSGPEVKKPGTSVKVSCKASGFTFMSSAVQWVRQARGQRLEWIGWIVIGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSSISCNDGFDIWGQGTMVTVS" heavyMask: type: string example: "26-32" lightChain: type: string example: "DVVMTQTPFSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPYTFGGGTKLEIK" lightMask: type: string example: "24-34" attention: type: boolean description: "Compute attention matrix with dimension [Layer x Heads x (Length + 2) x (Length + 2)] [Only available when task is one of antibody-embeddings, nanobody-embeddings]" default: False # Antibody-Annotation Settings AntibodyAnnotationSettings: type: object required: - task - heavySequence - lightSequence properties: task: type: string default: "antibody" enum: - "antibody" - "nanobody" heavySequence: type: string example: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" lightSequence: type: string example: "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIN" # Antibody-Diffusion-Properties Settings AntibodyDiffusionPropertiesSettings: type: object required: - pdbFile - property - numDesigns properties: pdbFile: type: string description: "Input antibody or nanobody file containing antigen and binder to design File with extensions [pdb]" format: binary sampleCDRTogether: type: boolean description: "If true, all 6 CDRs will be sampled simultaneously (mode: multiple_cdrs). If false, each CDR is sampled individually with property guidance." default: False property: type: string description: "Property to Optimize for" default: "DDG_Hydropathy" enum: - "DDG_Hydropathy" - "Hydropathy" - "DDG" numDesigns: type: number description: "Number of designs (sequence and structure codesign) to generate" default: 10 heavyChain: type: string description: "Chain ID for the heavy chain" example: "B" lightChain: type: string description: "Chain ID for the light chain" example: "A" scoring: type: string description: "Scoring analysis to perform on each designed structure" enum: - "binding-ddg" - "netsolp" - "temstapro" # Antibody-Evolution Settings AntibodyEvolutionSettings: type: object required: - sequence properties: sequence: type: string description: "Wildtype protein sequence you want to evolve" example: "QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSLAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARGGSVSGTLVDFDIWGQGTMVTVS" # Antidif Settings AntidifSettings: type: object required: - pdbFile - chains properties: pdbFile: type: string description: "pdb structure to find binding pocket File with extensions [pdb]" example: "9f6o.pdb" format: binary chains: type: array items: type: string description: "Chains to design" example: ["B"] numSamples: type: number description: "Number of samples to generate" default: 4 # Antifold Settings AntifoldSettings: type: object required: - task - pdbFile - heavyChain - lightChain - regions properties: task: type: string description: "Antibody or nanobody input" example: "nanobody" default: "antibody" enum: - "antibody" - "nanobody" pdbFile: type: string description: "Antibody pdb to design sequences for File with extensions [pdb]" example: "9f6o.pdb" format: binary heavyChain: type: string description: "ID in pdb file of heavy chain" example: "B" lightChain: type: string description: "ID in pdb file of light chain [Only available when task is one of antibody]" example: "L" includeAntigen: type: boolean description: "Include antigen chain in context of design" default: True antigenChain: type: string description: "Antigen chain to use in design of antibody/antigen complex" regions: type: string description: "Regions to mutate, separated by space (see https://github.com/oxpig/AntiFold?tab=readme-ov-file#imgt-regions-dict to find yours)" default: ['CDR1', 'CDR2', 'CDR3'] enum: - "all" - "allH" - "allL" - "FWH" - "FWL" - "CDRH" - "CDRL" - "FW1" - "FWH1" - "FWL1" - "CDR1" - "CDRH1" - "CDRL1" - "FW2" - "FWH2" - "FWL2" - "CDR2" - "CDRH2" - "CDRL2" - "FW3" - "FWH3" - "FWL3" - "CDR3" - "CDRH3" - "CDRL3" - "FW4" - "FWH4" - "FWL4" selectCustomResidues: type: boolean description: "Select custom residues to be designed" default: False customHeavyResidues: type: string customLightResidues: type: string temperature: type: number description: "Sampling temperature for sequences" minimum: 0 maximum: 1 default: 0.2 numSequences: type: number description: "Number of sequences to generate" default: 10 numBatches: type: integer description: "Will submit multiple parallel batches with numSequences designs each" maximum: 1000 default: 1 verifySequences: type: string description: "Automatically perform structure prediction on generated sequences for verification" enum: - "verify-alphafold" - "verify-chai" # Apm Settings ApmSettings: type: object required: - pdbFile - chainDesign properties: pdbFile: type: string description: "Pdb structure file to be designed - contains both protein and binder File with extensions [pdb]" example: "6qg8.pdb" format: binary chainDesign: type: string description: "Specify which chain to design (your binder chain)" example: "A" sampleNum: type: number default: 8 sampleLength: type: number description: "If the sample length is not specified the ground truth length is used" default: None randomCentering: type: boolean description: "Recommended for designing longer binders, could lead to significant variation between runs" default: False # Aqueous-Solubility Settings AqueousSolubilitySettings: type: object required: - smiles properties: smiles: type: string example: "CC(=O)c1ccc(O)cc1" # Atomsurf Settings AtomsurfSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure in pdb format File with extensions [pdb]" example: "1a3n.pdb" format: binary # Autodock-Vina Settings AutodockVinaSettings: type: object required: - receptorFile - ligandFile - boxX - boxY - boxZ - width - height - depth properties: receptorFile: type: string example: "1iep.pdb" format: binary ligandFile: type: string description: "sdf structure file for your ligand (one ligand per file) File with extensions [sdf]" example: "Conformer3D_COMPOUND_CID_5291.sdf" format: binary boxX: type: number description: "X coordinate of bounding box center" example: "15.190" default: 0 boxY: type: number description: "Y coordinate of bounding box center" example: "53.903" default: 0 boxZ: type: number description: "Z coordinate of bounding box center" example: "16.917" default: 0 width: type: number description: "Width of bounding box" example: "20" default: 10 height: type: number description: "Height of bounding box" example: "20" default: 10 depth: type: number description: "Depth of bounding box" example: "20" default: 10 exhaustiveness: type: number description: "Adjusts the amount of computational effort used during a docking experiment - increasing this to 32 will give a more consistent docking result" default: 8 # Balm-Finetune Settings BalmFinetuneSettings: type: object required: - csvFile - proteinColumn - drugColumn - labelColumn properties: csvFile: type: string format: binary proteinColumn: type: string description: "Column in CSV containing protein sequences" drugColumn: type: string description: "Column in CSV containing drug SMILES" labelColumn: type: string description: "Column in CSV containing label to predict (e.g. binding affinity)" # Balm-Inference Settings BalmInferenceSettings: type: object required: - csvFile - proteinColumn - drugColumn properties: csvFile: type: string description: "CSV with sequences to predict properties for File with extensions [csv]" format: binary proteinColumn: type: string description: "Column in CSV containing protein sequences" drugColumn: type: string description: "Column in CSV containing protein sequences" # Balm-Paired Settings BalmPairedSettings: type: object required: - model - heavySequence - lightSequence properties: model: type: string description: "Model to use" default: "ft-esm" enum: - "ft-esm" - "balm-paired" heavySequence: type: string example: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" lightSequence: type: string example: "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIN" # Bbmerge Settings BbmergeSettings: type: object required: - r1Fastq - r2Fastq properties: r1Fastq: type: string description: "Read 1 fastq file File with extensions [fastq, fastq.gz]" format: binary r2Fastq: type: string description: "Read 2 fastq file File with extensions [fastq, fastq.gz]" format: binary # Bde Settings BdeSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "Type of input to use File with extensions [sdf]" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string example: "CC(=O)c1ccc(O)cc1" sdfFile: type: string example: "c1cc(O)ccc1C(=O)C (Neutral Structure).sdf" format: binary # Bindcraft Settings BindcraftSettings: type: object required: - mode - pdbFile - chains properties: mode: type: string default: "default" enum: - "default" - "peptide" pdbFile: type: string description: "Protein structure of your target. Please trim to under 750 residues for optimal performance. File with extensions [pdb]" example: "PDL1.pdb" format: binary chains: type: array items: type: string description: "Target chains to design a binder to" example: ["A"] hotspotResidues: type: object description: "Specify hotspot residues for your binder to target as a binding site. If left empty suitable hotspots will be selected automatically" example: {'A': '1-10', 'B': '1-20'} maxLength: 600 numDesigns: type: integer description: "Number of designs to generate (1-16)" default: 1 binderLengthRange: type: array items: type: string description: "Range of binder length range to sample from" default: {'default': '70,150', 'peptide': '10,20'} rosetta: type: boolean description: "Get in touch at info@tamarind.bio if you have a license and would like to use Bindcraft with Rosetta" default: False omitAAs: type: string description: "which amino acids to exclude from design (note: they can still occur if no other options are possible in the position)" predictBigBang: type: boolean description: "Introduce atom position bias into the structure module for atom initilisation. Recommended if target and design are large (more than 600 amino acids)." weightsHelicity: type: number description: "Helix propensity of the design, Default 0, negative values bias towards beta sheets" minimum: -5 maximum: 5 trajectoryOnly: type: boolean description: "Run only the ColabDesign binder hallucination step without MPNN redesign and AlphaFold validation. Saves compute but produces unoptimized designs." default: False betasheetAdvancedSettings: type: boolean description: "Promote the design of more beta sheeted proteins, but requires more sampling" default: False mpnnAdvancedSettings: type: boolean description: "Use soluble MPNN to optimize the interface instead of Alphafold2" default: False flexibleAdvancedSettings: type: boolean description: "Greater flexibilty on both sidechain and backbone level for target template protocol" default: False hardtargetAdvancedSettings: type: boolean description: "Use initial guess to improve complex prediction for difficult targets, but might introduce some bias [Only available when mode is one of default]" default: False customAdvancedSettingsFile: type: string description: "Upload your own BindCraft advanced settings JSON file. This will override the checkbox advanced settings above if provided. File with extensions [json]" format: binary filterType: type: string description: "Relaxed filters are more permissive but may result in fewer experimental successes" default: {'default': 'default', 'peptide': 'peptide'} enum: - "default" - "relaxed" - "peptide" - "custom" customFiltersFile: type: string description: "Upload your own BindCraft filters JSON file. This will override the Filter Type dropdown above if provided. File with extensions [json]" format: binary pLDDT: type: number description: "pLDDT threshold for filtering designs (lower bound)" minimum: 0 maximum: 1 default: 0.8 pTM: type: number description: "pTM threshold for filtering designs (lower bound)" minimum: 0 maximum: 1 default: 0.55 ipTM: type: number description: "ipTM threshold for filtering designs (lower bound)" minimum: 0 maximum: 1 default: 0.5 i_pAE: type: number description: "i_pAE threshold for filtering designs (upper bound)" minimum: 0 maximum: 1 default: 0.35 Surface_Hydrophobicity: type: number description: "Surface_Hydrophobicity threshold for filtering designs (upper bound)" minimum: 0 maximum: 1 default: 0.35 n_InterfaceResidues: type: number description: "n_InterfaceResidues threshold for filtering designs (lower bound)" default: 7 n_InterfaceHbonds: type: number description: "n_InterfaceHbonds threshold for filtering designs (lower bound)" default: 3 Hotspot_RMSD: type: number description: "Hotspot_RMSD threshold for filtering designs (upper bound)" default: 6 Binder_pLDDT: type: number description: "Binder_pLDDT threshold for filtering designs (lower bound)" default: 0.8 Binder_RMSD: type: number description: "Binder_RMSD threshold for filtering designs (upper bound)" default: 3.5 minRunTime: type: number description: "Amount of time we will run your job before stopping it if no successful designs passing all filters are found" minimum: 0 maximum: 200 default: 16 # Binding-Ddg Settings BindingDdgSettings: type: object required: - wildtypeFile - mutantFile properties: wildtypeFile: type: string description: "Wildtype structure - must be the same length as mutant File with extensions [pdb]" format: binary mutantFile: type: string description: "Mutant structure - must be the same length as wildtype File with extensions [pdb]" format: binary # Bioemu Settings BioemuSettings: type: object required: - sequence properties: sequence: type: string example: "SAKIDNLD" maxLength: 600 numSamples: type: number default: 10 filter: type: boolean default: True # Biophi Settings BiophiSettings: type: object required: - task - heavySequence - lightSequence properties: task: type: string description: "Input type" default: "antibody" enum: - "antibody" heavySequence: type: string description: "Heavy sequence of your antibody" example: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" lightSequence: type: string description: "Light sequence of your antibody [Only available when task is one of antibody]" example: "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIN" threshold: type: string description: "OASis identity score of an antibody is calculated as the fraction of its 9-mer peptides that are considered Hum human. The prevalence threshold determines what fraction of human subjects from the Observed Numbe Antibody Space database should contain a given Kaba peptide in order for it to be considered human. The higher the threshold, the stricter the evaluation. [Only available when task is one of antibody]" default: "relaxed" enum: - "loose" - "relaxed" - "medium" - "strict" # Blast Settings BlastSettings: type: object required: - sequence properties: sequence: type: string description: "Protein sequence to search against the BLAST database. Should contain only valid amino acid codes." example: "DVQLQESGGGLVQAGGSLRLSCAVSGQTWTNYHIGWFRQAPGKARESVASIEWGGRGTYATDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAQSSSRSPLESNYDYWGQGTQVTVSSHHHHHHHH" maxLength: 10000 database: type: string description: "Database to search against" example: "nr" default: "nr" enum: - "nr" - "swissprot" - "landmark" - "pataa" - "pdbaa" - "env_nr" - "tsa_nr" evalue: type: number description: "Expectation value threshold for BLAST search. Lower values are more stringent (0.00001-0.1)" example: "0.001" minimum: 1e-05 maximum: 0.1 default: "0.001" maxTargetSeqs: type: number description: "Maximum number of sequences to report in BLAST results (1-100)" example: "50" minimum: 1 maximum: 100 default: "50" wordSize: type: number description: "Word size for initial matches in BLAST search (3-7)" example: "5" minimum: 3 maximum: 7 default: "5" gapCosts: type: string description: "Gap opening and extension costs for BLAST alignment, separated by a space (e.g., '11 1')" example: "11 1" default: "11 1" organism: type: string description: "Filter BLAST results by organism" example: "9606" default: "" enum: - "" - "3702" - "9913" - "6239" - "3055" - "7955" - "44689" - "7227" - "562" - "3052230" - "9606" - "10090" - "2104" - "4530" - "5833" - "4754" - "10116" - "4932" - "4896" - "9823" - "31033" - "8355" - "8364" - "4577" dnaSequence: type: boolean description: "Check if the input sequences are DNA sequences rather than protein sequences" example: False default: False # Boltz Settings BoltzSettings: type: object required: - inputFormat - yamlFile - sequence - molecules properties: inputFormat: type: string maxLength: 2048 default: "sequence" enum: - "sequence" - "list" - "molecules" - "yaml" yamlFile: type: string description: "Boltz YAML input file (see https://github.com/jwohlwend/boltz/blob/main/docs/prediction.md) File with extensions [yaml, yml] [Only available when inputFormat is one of yaml]" format: binary sequence: type: string description: "Protein sequence (use : to specify chainbreaks for multimers) [Only available when inputFormat is one of sequence]" example: "TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK:MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM" molecules: type: string example: ["{'type': 'protein', 'sequence': 'TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQIL', 'chain': 'A'}"] proteins: type: string description: "List of protein sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK", "MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM"] rnas: type: string description: "List of RNA sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["GAGAGAGAAGTCAACCAGAGAAACACACCAACCCATTGCACTCCGGG", "TTGGTGGTATATTACCTGGTACGGGGGAAACTTCGTGGTGGCCGGCCACCTGACA"] dnas: type: string description: "List of DNA sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["GAGAGAGAAGTCAACCAGAGAAACACACCAACCCATTGCACTCCGGG", "TTGGTGGTATATTACCTGGTACGGGGGAAACTTCGTGGTGGCCGGCCACCTGACA"] addLigands: type: boolean description: "Add small molecule ligands to your structure prediction" default: False ligands: type: string description: "Specify your ligands (CCD code or smiles), use : to separate multiple ligands in one structure prediction (ex. CC:CC). Each new line is a separate set of ligands, to be paired with each protein sequence. [Only available when inputFormat is one of list, sequence]" example: ["SAH", "N[C@@H](Cc1ccc(O)cc1)C(=O)O"] addDNA: type: boolean description: "Add DNA to your structure prediction" default: False dna: type: string description: "DNA to include in your complex (use : to separate multiple DNA sequences)" example: "GAGAGAGAAGTCAACCAGAGAAACACACCAACCCATTGCACTCCGGG" fastaFile: type: string description: "Fasta file with sequences in complex (see https://github.com/jwohlwend/boltz/blob/main/docs/prediction.md) File with extensions [fa, fasta] [Only available when inputFormat is one of fasta]" format: binary numSamples: type: number description: "Number of samples n/5 trunk recycles will be performed with 5 diffusion samples each" maximum: 200 default: 5 numBatches: type: integer description: "Will submit multiple parallel batches with numSamples designs each" maximum: 1000 default: 1 numRecycles: type: number description: "Number of recycles to perform during inference" default: 3 predictAffinity: type: boolean description: "Calculate binding affinity for each design (only available for small molecule binders)" default: False binderChain: type: string description: "Chain ID of the binder (must be a small molecule ligand present in your input). Chain IDs are assigned in the order they appear in the input. For example, if you have 2 protein chains and 1 ligand, the binder chain will be C." example: "A" stepScale: type: number description: "Lower step scale means more diversity (recommended between 1 and 2)" default: 1.638 seed: type: number description: "Seed for inference" bonds: type: object description: "" example: ["{'atom2Atom': 'N', 'atom2Idx': '1', 'atom1Idx': '32', 'atom2Chain': 'B', 'atom1Atom': 'C', 'atom1Chain': 'A'}"] default: [] pocketRestraints: type: object description: "" example: ["{'binderChain': 'A', 'pocketChain': 'B', 'pocketContacts': '5 6 7'}"] default: [] modifications: type: object description: "Post-translational modifications to apply to the protein" example: ["{'modification': 'PTM', 'chain': 'A', 'position': '15'}"] default: [] contactRestraints: type: object description: "" example: ["{'binderChain': 'A', 'pocketChain': 'B', 'pocketContacts': '5 6 7'}"] default: [] logan: type: boolean description: "Use BFVD Logan MSA for prediction" outputType: type: string description: "Output type" enum: - "pdb" - "mmcif" version: type: string description: "Version of boltz code to use (https://github.com/jwohlwend/boltz/releases)" default: "2.2.1" enum: - "2.2.1" - "1.0.0" - "0.4.0" cyclicPeptide: type: boolean description: "Automatically set the shortest protein chain to be cyclic for cyclic peptide prediction" default: False templateFiles: type: string description: "Use custom structural templates in your prediction File with extensions [cif]" format: binary templateMapping: type: string description: "Specify which chains in the template files should be used for which chains in the target. Note: In batch jobs, all protein sequences will use the same template files. If you need different templates for different sequences, please submit separate batch jobs." example: ["{'templateName': 'input.cif', 'mappings': [{'boltzChainID': 'A', 'templateChainID': 'B'}]}"] templateDistanceThreshold: type: number description: "Distance threshold for template files" a3mFiles: type: string description: "Upload custom a3m (multiple sequence alignment) files to use instead of generating MSAs automatically. Each a3m file should correspond to a protein chain in your complex. File with extensions [a3m]" format: binary a3mMapping: type: object description: "Specify which chain each a3m file corresponds to. Chain IDs are assigned in the order they appear in the input (e.g., A, B, C). Note: In batch jobs, all sequences will use the same a3m files. If you need different MSAs for different sequences, please submit separate batch jobs." example: ["{'boltzChainID': 'A', 'a3mName': 'protein_chain_a.a3m'}", "{'boltzChainID': 'B', 'a3mName': 'protein_chain_b.a3m'}"] method: type: string description: "Method to use for prediction, conditions predicted structure" enum: - "md" - "x-ray diffraction" - "electron microscopy" - "solution nmr" - "solid-state nmr" - "neutron diffraction" - "electron crystallography" - "fiber diffraction" - "powder diffraction" - "infrared spectroscopy" - "fluorescence transfer" - "epr" - "theoretical model" - "solution scattering" - "other" - "afdb" - "boltz-1" chooseBest: type: boolean description: "Return only the best confidence model (model_0) or all generated models" default: True maxMsaSeqs: type: number description: "Max number of sequences to use for MSA, use less for a more shallow MSA< which may result in prediction closer to your template" usePotentials: type: boolean description: "Whether to run the original Boltz-2 model using inference time potentials (significantly improve the physical quality of the poses)" default: False useMSA: type: boolean description: "When MSAs are disabled, Boltz will not use MSA data for prediction." default: True msaDatabase: type: string description: "Select how the MSA is generated using UniRef30, SwissProt, and the ColabFold environmental database." example: "uniref" default: "uniref" enum: - "uniref" - "swissprot" - "uniref+swissprot" runIpsae: type: boolean description: "Generate IPSAE metrics for protein-protein complex interfaces" default: True # Boltz-Finetune Settings BoltzFinetuneSettings: type: object required: - proteinFiles properties: proteinFiles: type: string description: "cif files or zip file containing cif files to use for finetuning File with extensions [cif, zip]" format: binary # Boltzdesign Settings BoltzdesignSettings: type: object required: - inputFormat - pdbFile - targetChains - targetMols - targetType - customTargetInput properties: inputFormat: type: string default: "pdb" enum: - "pdb" - "sequence" - "small_molecule" pdbFile: type: string description: "Target pdb to design File with extensions [pdb] [Only available when inputFormat is one of pdb, small_molecule]" example: "7v11.pdb" format: binary targetChains: type: array items: type: string description: "chains to design a binder for [Only available when inputFormat is one of pdb]" example: ["A"] default: [] numDesigns: type: integer description: "Number of binders to generate" default: 1 targetMols: type: string description: "Select ligands to target from your pdb [Only available when inputFormat is one of small_molecule]" example: "OQO" targetType: type: string description: "Custom target input type [Only available when inputFormat is one of sequence, pdb]" default: "protein" enum: - "protein" - "rna" - "dna" - "small_molecule" - "metal" customTargetInput: type: string description: "Enter target sequences/SMILES (comma-separated for multiple, (e.g. \"ATGC, TACG\") [Only available when inputFormat is one of sequence]" example: "OQO" binderLengthRange: type: array items: type: string description: "Range of binder length range to sample from" default: "100,150" constraintChain: type: string description: "Chain to constrain the binder to [Only available when inputFormat is one of pdb]" constraintResidues: type: string description: "Select residues to constrain the binder to [Only available when inputFormat is one of pdb]" modifications: type: object # Boltzgen Settings BoltzgenSettings: type: object required: - binderType - targetFile - designRegions - cyclotideSequence - disulfideBonds - targetSmiles - scaffold - scaffoldSubType - frameworkInputType - frameworkSequence - frameworkFile - lengthRange - smbLengthRange - smbFrameworkInputType - smbFrameworkSequence - smbFrameworkFile - entities - yamlFile - numStructureFiles - structureFile - structureFiles - protocol - numDesigns properties: binderType: type: string default: "de-novo-nanobody" enum: - "de-novo-nanobody" - "de-novo-antibody" - "protein" - "small-molecule-binder" - "peptide" - "cyclotide" - "protein-redesign" - "custom" - "yaml" targetFile: type: string description: "Target structure file to design the binder for File with extensions [pdb] [Only available when binderType is one of de-novo-nanobody, de-novo-antibody, protein, peptide, cyclotide, protein-redesign]" example: {'peptide': '5cqg.pdb', 'cyclotide': '5cqg.pdb', 'protein-redesign': '7rpz.pdb', 'de-novo-nanobody': '9bkq-assembly2.pdb', 'de-novo-antibody': '9bkq-assembly2.pdb', 'protein': '7rpz.pdb'} format: binary targetChains: type: array items: type: string description: "Chains to design the binder for [Only available when binderType is one of de-novo-nanobody, de-novo-antibody, protein, peptide, cyclotide, protein-redesign]" bindingSite: type: object description: "Residues to design the binder for [Only available when binderType is one of de-novo-nanobody, de-novo-antibody, protein, peptide, cyclotide]" designRegions: type: object description: "Select which residues on the target structure to redesign. These regions will be redesigned while keeping the rest of the structure fixed. [Only available when binderType is one of protein-redesign]" notBindingSite: type: object description: "Residues that are not part of the binding site [Only available when binderType is one of de-novo-nanobody, de-novo-antibody, protein, peptide, cyclotide]" cyclotideSequence: type: string description: "Sequence specification with cysteines for disulfide bonds (e.g., '3C8C6C5C3C1C2' means 3 residues, Cys, 8 residues, Cys, etc.) [Only available when binderType is one of cyclotide]" example: {'cyclotide': '3C8C6C5C3C1C2'} disulfideBonds: type: object description: "Pairs of cysteine positions to form disulfide bonds [Only available when binderType is one of cyclotide]" example: ["{'position1': 4, 'position2': 26}", "{'position1': 13, 'position2': 30}", "{'position1': 20, 'position2': 32}"] targetSmiles: type: string description: "Target SMILES string to design the binder for [Only available when binderType is one of small-molecule-binder]" example: {'small-molecule-binder': 'N[C@@H](Cc1ccc(O)cc1)C(=O)O'} scaffold: type: string description: "Choose default (use default scaffolds) or custom (redesign existing framework) [Only available when binderType is one of de-novo-nanobody, de-novo-antibody, protein]" default: "default" enum: - "default" - "custom" smbScaffold: type: string description: "Optionally use an antibody or nanobody scaffold with CDR design instead of a de novo protein binder [Only available when binderType is one of small-molecule-binder]" default: "none" enum: - "none" - "default" - "custom" scaffoldSubType: type: string description: "Choose whether to use nanobody (single chain) or antibody (heavy + light chain) scaffolds [Only available when binderType is one of small-molecule-binder]" default: "nanobody" enum: - "nanobody" - "antibody" frameworkInputType: type: string description: "Choose whether to provide a framework structure or sequence - examples scaffolds are used by default for nanobody/antibody, no scaffold is used for protein [Only available when binderType is one of de-novo-nanobody, de-novo-antibody, protein]" default: "structure" enum: - "structure" - "sequence" frameworkSequence: type: string description: "Framework sequence with CDR placeholders. Use number ranges (e.g., 5..10) to specify variable-length CDR regions. [Only available when binderType is one of de-novo-nanobody, protein]" example: {'de-novo-nanobody': 'EVQLVESGGGLVQPGGSLRLSCAASG5..10WVRQAPGKGLEWVS8..12RFTISRDNSKNTLYLQMNSLRAEDTAVYYC10..20WGQGTLVTVSS'} frameworkHeavySequence: type: string description: "Heavy chain framework sequence with CDR placeholders. [Only available when binderType is one of de-novo-antibody]" example: {'de-novo-antibody': 'EVQLVESGGGLVQPGRSLRLSCAASG7..9WVRQAPGKGLEWVS5..8RFTISRDNAKNSLYLQMNSLRAEDTAVYYC3..21WGQGTLVTVSS'} frameworkLightSequence: type: string description: "Light chain framework sequence with CDR placeholders. [Only available when binderType is one of de-novo-antibody]" example: {'de-novo-antibody': 'DIQMTQSPSSLSASVGDRVTITC10..17WYQQKPGKAPKLLIY7GVPSRFSGSGSGTDFTLTISSLQPEDVATYYC8..12FGQGTKVEIK'} frameworkFile: type: string description: "Framework structure (docked pose or existing residues of redesigned portions will not be used) File with extensions [pdb] [Only available when binderType is one of de-novo-nanobody, de-novo-antibody, protein]" example: {'de-novo-nanobody': '7eow.pdb', 'de-novo-antibody': '6cr1.pdb'} format: binary frameworkChain: type: string description: "Chain ID of the nanobody framework structure. Only for nanobody scaffold type. [Only available when binderType is one of de-novo-nanobody]" example: {'de-novo-nanobody': 'B'} frameworkHeavyChain: type: string description: "Chain ID of the heavy chain. [Only available when binderType is one of de-novo-antibody]" example: {'de-novo-antibody': 'B'} frameworkLightChain: type: string description: "Chain ID of the light chain. [Only available when binderType is one of de-novo-antibody]" example: {'de-novo-antibody': 'A'} cdrRegions: type: string description: "Select CDR regions to redesign. Only for nanobody scaffold type. [Only available when binderType is one of de-novo-nanobody]" example: {'de-novo-nanobody': '26-34,52-59,98-118'} heavyCDRRegions: type: string description: "Select heavy chain CDR regions to redesign. [Only available when binderType is one of de-novo-antibody]" example: {'de-novo-antibody': '26-32,52-57,99-110'} lightCDRRegions: type: string description: "Select light chain CDR regions to redesign. [Only available when binderType is one of de-novo-antibody]" example: {'de-novo-antibody': '24-34,50-56,89-97'} cdrExcludeCounts: type: string description: "Comma-separated: number of residues to remove from start of each CDR (e.g., '3,3,7') [Only available when binderType is one of de-novo-nanobody]" example: {'de-novo-nanobody': '3,3,7'} cdrInsertionLengths: type: string description: "Comma-separated ranges for new residues per CDR (e.g., '1-5,1-5,1-14') [Only available when binderType is one of de-novo-nanobody]" example: {'de-novo-nanobody': '1-5,1-5,1-14'} heavyCDRExcludeCounts: type: string description: "Comma-separated: number of residues to remove from start of each heavy CDR (e.g., '7,6,12') [Only available when binderType is one of de-novo-antibody]" example: {'de-novo-antibody': '7,6,12'} heavyCDRInsertionLengths: type: string description: "Comma-separated ranges for new residues per heavy CDR (e.g., '7-9,5-8,3-21') [Only available when binderType is one of de-novo-antibody]" example: {'de-novo-antibody': '7-9,5-8,3-21'} lightCDRExcludeCounts: type: string description: "Comma-separated: number of residues to remove from start of each light CDR (e.g., '11,7,9') [Only available when binderType is one of de-novo-antibody]" example: {'de-novo-antibody': '11,7,9'} lightCDRInsertionLengths: type: string description: "Comma-separated ranges for new residues per light CDR (e.g., '10-17,7,8-12') [Only available when binderType is one of de-novo-antibody]" example: {'de-novo-antibody': '10-17,7,8-12'} lengthRange: type: array items: type: string description: "Range of lengths to sample from [Only available when binderType is one of protein, peptide, custom]" example: {'peptide': '12,20', 'protein': '100,150'} default: {'peptide': '10,20', 'protein': '100,150'} smbLengthRange: type: array items: type: string description: "Range of lengths to sample from [Only available when binderType is one of small-molecule-binder]" example: "140,180" default: "100,150" smbFrameworkInputType: type: string description: "Choose whether to provide a framework structure or sequence [Only available when binderType is one of small-molecule-binder]" default: "structure" enum: - "structure" - "sequence" smbFrameworkSequence: type: string description: "Heavy chain framework sequence with CDR placeholders. Use number ranges (e.g., 5..10) to specify variable-length CDR regions. [Only available when binderType is one of small-molecule-binder]" example: {'small-molecule-binder': 'EVQLVESGGGLVQPGGSLRLSCAASG5..10WVRQAPGKGLEWVS8..12RFTISRDNSKNTLYLQMNSLRAEDTAVYYC10..20WGQGTLVTVSS'} smbFrameworkFile: type: string description: "Framework structure file File with extensions [pdb] [Only available when binderType is one of small-molecule-binder]" format: binary smbFrameworkChain: type: string description: "Chain ID of the heavy chain in the framework structure. [Only available when binderType is one of small-molecule-binder]" smbCdrRegions: type: string description: "Select CDR regions to redesign. For antibody, these are the heavy chain CDR regions. [Only available when binderType is one of small-molecule-binder]" smbCdrExcludeCounts: type: string description: "Comma-separated: number of residues to remove from start of each CDR (e.g., '3,3,7') [Only available when binderType is one of small-molecule-binder]" smbCdrInsertionLengths: type: string description: "Comma-separated ranges for new residues per CDR (e.g., '1-5,1-5,1-14') [Only available when binderType is one of small-molecule-binder]" smbFrameworkLightSequence: type: string description: "Light chain framework sequence with CDR placeholders. [Only available when binderType is one of small-molecule-binder]" example: {'small-molecule-binder': 'DIQMTQSPSSLSASVGDRVTITC10..17WYQQKPGKAPKLLIY7GVPSRFSGSGSGTDFTLTISSLQPEDVATYYC8..12FGQGTKVEIK'} smbFrameworkLightChain: type: string description: "Chain ID of the light chain. [Only available when binderType is one of small-molecule-binder]" smbLightCDRRegions: type: string description: "Select light chain CDR regions to redesign. [Only available when binderType is one of small-molecule-binder]" smbLightCDRExcludeCounts: type: string description: "Comma-separated: number of residues to remove from start of each light CDR [Only available when binderType is one of small-molecule-binder]" smbLightCDRInsertionLengths: type: string description: "Comma-separated ranges for new residues per light CDR [Only available when binderType is one of small-molecule-binder]" cyclic: type: boolean description: "Whether the peptide should be cyclic [Only available when binderType is one of peptide]" default: False entities: type: object description: "List of protein and ligand entities to design [Only available when binderType is one of custom]" example: ["{'type': 'protein', 'sequence': '15..20', 'id': 'A'}", "{'type': 'ligand', 'ccd': 'WHL', 'id': 'B'}"] constraints: type: object description: "Optional list of structural constraints (bonds between atoms or total length constraints) [Only available when binderType is one of custom]" example: ["{'bond': {'atom2': ['B', 1, 'CK'], 'atom1': ['A', 4, 'SG']}}"] yamlFile: type: string description: "YAML file containing the configuration for the design task File with extensions [yaml, yml] [Only available when binderType is one of yaml]" format: binary numStructureFiles: type: string description: "Choose whether to provide one or multiple structure files File with extensions [pdb, cif] [Only available when binderType is one of yaml]" default: "1" enum: - "1" - "multiple" structureFile: type: string format: binary structureFiles: type: string description: "Multiple structure files for the YAML configuration File with extensions [pdb, cif] [Only available when binderType is one of yaml]" format: binary protocol: type: string description: "Select the protocol type for the YAML configuration [Only available when binderType is one of yaml]" default: "nanobody-anything" enum: - "nanobody-anything" - "protein-anything" - "protein-small_molecule" - "peptide-anything" numDesigns: type: number description: "Number of designs to generate" minimum: 1 maximum: 100000 default: 10 maxDesignsPerJob: type: number description: "Maximum number of designs per job when design batching is enabled. Used as threshold for auto-enabling batching and as default batch size." default: 10 designBatching: type: boolean description: "Automatically split large numDesigns into multiple jobs for better performance (auto-enabled when numDesigns > 10)" default: False designBatchSize: type: number description: "Maximum number of designs per job. Total designs will be split into multiple jobs of this size." maximum: 100 default: 10 budget: type: number description: "Final number of designed optimized for diversity and quality - taken among all batches" default: 2 omitAAs: type: string description: "Amino acids to omit from the design (C by default for peptide and nanobody design, none for others, use string 'empty' to omit no amino acids for nanobody/peptide)" runIpsae: type: boolean description: "Generate IPSAE metrics for protein-protein complex interfaces" default: True pae_cutoff: type: number description: "Cutoff for PAE in IPSAE scoring" default: 10 dist_cutoff: type: number description: "Cutoff for distance in IPSAE scoring" default: 10 # Caliby Settings CalibySettings: type: object required: - task - provideEnsembles - generateEnsembles - ensembleDir - numSeqsPerPdb - numSamplesPerPdb properties: task: type: string default: "Sequence Design" enum: - "Sequence Design" - "Scoring" inputFiles: type: string description: "Pdb/cif files or zip file containing structures to design File with extensions [pdb, cif, zip] [Only available when task is one of Sequence Design, Scoring]" format: binary provideEnsembles: type: boolean description: "Provide your own ensembles for the sequence design [Only available when task is one of Sequence Design, Scoring]" default: False generateEnsembles: type: boolean description: "Generate ensembles using Protpardelle-1c for the sequence design [Only available when task is one of Sequence Design]" default: True ensembleDir: type: string description: "Zip file containing your top level ensemble structures formatted according to the instructions (see github page) File with extensions [zip] [Only available when task is one of Sequence Design, Scoring]" format: binary numSeqsPerPdb: type: number description: "Number of sequences to design per PDB structure input [Only available when task is one of Sequence Design]" default: "4" numSamplesPerPdb: type: string description: "Number of ensembles to generate using Protpardelle-1c for the sequence design [Only available when task is one of Sequence Design]" default: "32" enum: - "8" - "16" - "32" - "64" omitAAs: type: string description: "These amino acids will be avoided when generating sequences [Only available when task is one of Sequence Design]" example: ["C", "G"] default: "" posConstraintCsv: type: string description: "CSV file containing position level constraints for the input PDBs formatted according to the instructions (see github page) File with extensions [csv] [Only available when task is one of Sequence Design]" format: binary # Catpred Settings CatpredSettings: type: object required: - sequence - smiles properties: sequence: type: string description: "Enzyme sequence to assess properties" example: "MLDDRARMEAAKKEKVEQILAEFQLQEEDLKKVMRRMQKEMDRGLRLETHEEASVKMLPTYVRSTPEGSEVGDFLSLDLGGTNFRVMLVKVGEGEEGQWSVKTKHQMYSIPEDAMTGTAEMLFDYISECISDFLDKHQMKHKKLPLGFTFSFPVRHEDIDKGILLNWTKGFKASGAEGNNVVGLLRDAIKRRGDFEMDVVAMVNDTVATMISCYYEDHQCEVGMIVGTGCNACYMEEMQNVELVEGDEGRMCVNTEWGAFGDSGELDEFLLEYDRLVDESSANPGQQLYEKLIGGKYMGELVRLVLLRLVDENLLFHGEASEQLRTRGAFETRFVSQVESDTGDRKQIYNILSTLGLRPSTTDCDIVRRACESVSTRAAHMCSAGLAGVINRMRESRSEDVMRITVGVDGSVYKLHPSFKERFHASVRRLTPSCEITFIESEEGSGRGAALVSAVACKKACMLGQ" smiles: type: string example: "C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O" # Chai Settings ChaiSettings: type: object required: - inputFormat - sequence - molecules properties: inputFormat: type: string default: "sequence" enum: - "sequence" - "molecules" - "list" sequence: type: string description: "Protein sequence (use : to specify chainbreaks for multimers) [Only available when inputFormat is one of sequence]" example: "TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK:MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM" maxLength: 2048 molecules: type: string example: ["{'type': 'protein', 'sequence': 'TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQIL', 'chain': 'A'}"] proteins: type: string description: "List of protein sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK", "MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM"] rnas: type: string description: "List of RNA sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["GAGAGAGAAGTCAACCAGAGAAACACACCAACCCATTGCACTCCGGG", "TTGGTGGTATATTACCTGGTACGGGGGAAACTTCGTGGTGGCCGGCCACCTGACA"] dnas: type: string description: "List of DNA sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["GAGAGAGAAGTCAACCAGAGAAACACACCAACCCATTGCACTCCGGG", "TTGGTGGTATATTACCTGGTACGGGGGAAACTTCGTGGTGGCCGGCCACCTGACA"] ligands: type: string description: "List of ligands sequences you want included in your complex (smiles), use : to separate multiple ligands [Only available when inputFormat is one of list, sequence]" example: ["N[C@@H](Cc1ccc(O)cc1)C(=O)O"] useMSA: type: boolean description: "When MSAs are disabled, Chai-1 uses a language model to capture evolutionary statistics about the protein. The authors find that this has about 90% of the accuracy of the tool, but is faster to produce a result. We use a version of ColabFold/MMseqs2 server that we host ourselves for the MSA step." default: True pdb100Templates: type: boolean default: False templateFiles: type: string description: "Use custom structural templates in your prediction. Must also fill in Custom Template Chain Mapping. File with extensions [cif]" format: binary templateMapping: type: object description: "For each custom template uploaded, indicate the name of the chain in your prediction and the name of the chain in your template file" pocketRestraints: type: object description: "Restrain any residue on chain B to chain A" example: ["{'chainB': 'B', 'chainA': 'A', 'res_idxA': 1}"] contactRestraints: type: object description: "Restrain a specific residue on chain A to chain B" example: ["{'res_idxB': 1, 'chainB': 'B', 'chainA': 'A', 'res_idxA': 1}"] covalentRestraints: type: object description: "Create a covalent bond between an atom on chain A and an atom on chain B" example: ["{'res_idxB': 1, 'covalentAtomA': 'C', 'covalentAtomB': 'C', 'chainB': 'B', 'chainA': 'A', 'res_idxA': 1}"] restraintsMinDistance: type: number description: "Minimum distance for restraints" example: 0 restraintsMaxDistance: type: number description: "Maximum distance for restraints" example: 5 modifications: type: object numSamples: type: number description: "Number of samples n/5 trunk recycles will be performed with 5 diffusion samples each" maximum: 200 default: 5 numTrunkSamples: type: number description: "Total number of samples will be numTrunkSamples x numSamples" maximum: 100 default: 1 numBatches: type: integer description: "Will submit multiple parallel batches with numSamples designs each" maximum: 1000 default: 1 numRecycles: type: number default: 3 seed: type: number description: "Random seed to use with inference" logan: type: boolean description: "Use BFVD Logan MSA for prediction" msaDatabase: type: string description: "Select how the MSA is generated using UniRef30, SwissProt, and the ColabFold environmental database." example: "uniref" default: "uniref" enum: - "uniref" - "swissprot" - "uniref+swissprot" # Charge-Dipole Settings ChargeDipoleSettings: type: object required: - inputType - smiles - sdfFile - xyzFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" - "xyz" smiles: type: string description: "SMILES string of the molecule [Only available when inputType is one of smiles]" example: "CCO" sdfFile: type: string description: "SDF/MOL file with 3D coordinates File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary xyzFile: type: string description: "XYZ coordinate file (e.g. from geometry optimization) File with extensions [xyz] [Only available when inputType is one of xyz]" format: binary chargeMethod: type: string description: "Charge partitioning scheme. Mulliken/Lowdin require QM calculation. Gasteiger is fast (no QM needed)" default: "mulliken" enum: - "mulliken" - "lowdin" - "gasteiger" method: type: string description: "Quantum chemistry method for Mulliken/Lowdin charges. g-xTB: gas-phase only" default: "xtb-gfn2" enum: - "xtb-gfn2" - "g-xtb" - "b3lyp" - "wb97x-d3" basisSet: type: string description: "Basis set for DFT charge calculation. Larger basis = more accurate charges" default: "def2-svp" enum: - "def2-svp" - "def2-svpd" - "def2-tzvp" - "def2-tzvpd" charge: type: number description: "Net molecular charge" default: 0 multiplicity: type: number description: "Spin multiplicity (2S+1). Use values > 1 for open-shell systems to compute spin density" default: 1 solvent: type: string description: "Implicit solvation environment" default: "none" enum: - "none" - "water" - "acetonitrile" - "dmso" - "methanol" - "ethanol" - "chloroform" - "toluene" - "thf" - "dichloromethane" preOptimize: type: boolean description: "Run a fast xTB geometry optimization first. Recommended for SMILES input" default: True # Chembl Settings ChemblSettings: type: object required: - searchBy - smiles - name - chemblId properties: searchBy: type: string description: "Select which type of input to search by" default: "SMILES" enum: - "SMILES" - "Name" - "ChemBL ID" smiles: type: string description: "SMILES string to search against the ChemBL database [Only available when searchBy is one of SMILES]" example: "CC(=O)Oc1ccccc1C(=O)O" maxResults: type: number description: "Maximum number of results to report (1-100) [Only available when searchBy is one of SMILES]" example: "50" minimum: 1 maximum: 100 default: "50" similarityThreshold: type: number description: "Similarity threshold for the results (0-1) [Only available when searchBy is one of SMILES]" example: "0.7" minimum: 0 maximum: 1 default: "0.7" name: type: string description: "Name of the compound to search for in the ChemBL database [Only available when searchBy is one of Name]" example: "ibuprofen" chemblId: type: string description: "ChemBL ID to search for in the the ChemBL database [Only available when searchBy is one of ChemBL ID]" example: "CHEMBL521" # Cluster-Pdbs Settings ClusterPdbsSettings: type: object required: - pdbFiles - clusterChains - rmsdCutoff - align - alignChains properties: pdbFiles: type: string description: "PDB files or trajectory to cluster File with extensions [pdb]" example: "5UOI.pdb" format: binary clusterChains: type: array items: type: string description: "Chain IDs to use for RMSD (e.g. A)." example: ["A"] rmsdCutoff: type: number description: "Root mean square deviation cutoff for cluster membership" default: 3 align: type: boolean description: "Align structures to the first pdb/frame before clustering" default: False alignChains: type: array items: type: string description: "Chains to align on." # Colabdock Settings ColabdockSettings: type: object required: - proteinFile1 - proteinFile2 properties: proteinFile1: type: string description: "Pdb structure files to dock File with extensions [pdb]" format: binary proteinFile2: type: string description: "Pdb structure files to dock File with extensions [pdb]" format: binary rest_1v1: type: object description: "1v1 restraint - Keep residue A close to residue B" example: ["{'residueB': 15, 'residueA': 4}"] rest_1vN: type: object description: "1vN restraint: Keep residue A close to one of residues B in range" example: ["{'start': 13, 'residueA': 4, 'end': 18}"] rest_MvN: type: number description: "Minimum number of 1vN restraints that must be satisfied" example: 1 rest_rep: type: object description: "Repulsive restraint - Keep residue A far from residue B" example: ["{'residueB': 18, 'residueA': 6}"] restraintThreshold: type: number description: "Distance threshold for attractive restraints (1v1, 1vN, MvN)" example: 8 default: 8 repulseThreshold: type: number description: "Distance threshold for repulsive restraints" example: 8 default: 8 # Conformer-Generation Settings ConformerGenerationSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string description: "SMILES string of the molecule [Only available when inputType is one of smiles]" example: "c1ccccc1CC(=O)O" sdfFile: type: string description: "SDF file (can contain initial conformers) File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary generationMethod: type: string description: "rdkit: fast distance-geometry + force field (~10s). crest: thorough GFN2 metadynamics search, best for flexible molecules (~10min)" default: "rdkit" enum: - "rdkit" - "crest" forceField: type: string description: "Force field for RDKit conformer optimization. MMFF94 is better for drug-like molecules, UFF is more universal" default: "mmff94" enum: - "mmff94" - "uff" numConformers: type: number description: "Maximum number of conformers to generate" default: 50 clustering: type: string description: "How to group similar conformers. rmsd: by 3D structure. energy: by energy. tfd: by torsion angles" default: "none" enum: - "none" - "rmsd" - "energy" - "tfd" clusterThreshold: type: number description: "RMSD threshold (Angstrom) or energy threshold (kcal/mol) for clustering" default: 0.5 energyScreening: type: string description: "Re-rank conformers using a more accurate energy method after generation" default: "none" enum: - "none" - "mmff" - "xtb-gfn2" - "g-xtb" - "r2scan-3c" energyWindow: type: number description: "Discard conformers more than this many kcal/mol above the lowest-energy conformer" default: 10 solvent: type: string description: "Solvent environment for energy screening (only used when energy screening is enabled)" default: "none" enum: - "none" - "water" - "acetonitrile" - "dmso" - "methanol" - "ethanol" - "chloroform" - "toluene" - "thf" - "dichloromethane" pruneSimilar: type: boolean description: "Remove near-duplicate conformers that are too similar in 3D structure" default: True pruneThreshold: type: number description: "Conformers with RMSD below this threshold (in Angstrom) are considered duplicates" default: 0.3 # Contact-Ms Settings ContactMsSettings: type: object required: - pdbFile - binderChains - targetChains properties: pdbFile: type: string description: "PDB file containing the binder-target complex File with extensions [pdb]" example: "7DK2_AB_C.pdb" format: binary binderChains: type: array items: type: string description: "Chain ID(s) of the binder molecule" example: ["A", "B"] targetChains: type: array items: type: string description: "Chain ID(s) of the target molecule" example: ["C"] # Cryfold Settings CryfoldSettings: type: object required: - map - sequence properties: map: type: string description: "CryoEM density map to use in structure prediction File with extensions [mrc]" format: binary sequence: type: string description: "Protein sequence" # Cryodrgn Settings CryodrgnSettings: type: object required: - particles - poses - apix properties: particles: type: string description: "Particles from CryoEM File with extensions [mrcs, star, cs]" format: binary poses: type: string description: "CTF and Poses of your particles File with extensions [cs, star, pkl]" format: binary apix: type: number description: "Angstrom/pixel" default: 1.03 # Custom-Msa Settings CustomMsaSettings: type: object required: - sequence - databaseFastaFile properties: sequence: type: string description: "Protein amino acid sequence" example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" databaseFastaFile: type: string description: "Sequences to use as database for custom MSA query File with extensions [fasta, fa]" format: binary numModels: type: number description: "Number of models to generate with Alphafold" default: 5 numRecycles: type: number description: "Number of recycles to use for each structure" default: 3 relax: type: boolean description: "Perform amber relaxation for more accurate side chain predictions" default: False # Dayhoff Settings DayhoffSettings: type: object required: - task - sequence properties: task: type: string default: "Guided Generation" enum: - "Guided Generation" - "Unconditional Generation" sequence: type: string description: "Protein amino acid sequence [Only available when task is one of Guided Generation]" example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" maxLength: 5000 maxLength: type: number default: 100 nGenerations: type: number default: 10 temperature: type: number description: "Sampling temperature for sequences" default: 5 minP: type: number description: "Minimum probability for sampling" minimum: 0 maximum: 1 default: 0 model: type: string description: "Model to use for the prediction" default: "Dayhoff-170m-BRq" enum: - "Dayhoff-170m-UR50" - "Dayhoff-170m-UR90" - "Dayhoff-170m-GR" - "Dayhoff-170m-UR50-BRu" - "Dayhoff-170m-UR50-BRq" - "Dayhoff-170m-UR50-BRn" - "Dayhoff-3b-UR90" - "Dayhoff-3b-GR-HM" - "Dayhoff-3b-GR-HM-c" # Deep-Viscosity Settings DeepViscositySettings: type: object required: - heavySequence - lightSequence properties: heavySequence: type: string description: "Heavy sequence of your antibody" example: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" lightSequence: type: string description: "Light sequence of your antibody" example: "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIN" # Deepfri Settings DeepfriSettings: type: object required: - task - sequence - pdbFile - ontology properties: task: type: string default: "sequence" enum: - "sequence" - "PDB" sequence: type: string description: "Protein amino acid sequence, place a : between chains for multimers [Only available when task is one of sequence]" example: "SMTDLLSAEDIKKAIGAFTAADSFDHKKFFQMVGLKKKSADDVKKVFHILDKDKDGFIDEDELGSILKGFSSDARDLSAKETKTLMAAGDKDGDGKIGVEEFSTLVAES" pdbFile: type: string description: "Structure to analyze File with extensions [pdb] [Only available when task is one of PDB]" example: "1s3p.pdb" format: binary ontology: type: string default: ['mf'] enum: - "mf" - "bp" - "cc" - "ec" saliency: type: boolean description: "Whether to compute class activation maps (will output a .json file)" default: False sequenceBatching: type: boolean description: "Batch process the input sequences" default: False sequenceBatchSize: type: number description: "Determines the number of sequences in each batch" # Deepimmuno Settings DeepimmunoSettings: type: object required: - sequence properties: sequence: type: string description: "Protein sequence to predict immunogenicity (highest result from every 9-mer will be returned)" example: "HPPLMNVER" hlas: type: string description: "HLA alleles to predict immunogenicity for (all by default)" example: ["HLA-A*0201"] default: ['HLA-A*0101', 'HLA-A*0201', 'HLA-A*0203', 'HLA-A*0205', 'HLA-A*0206', 'HLA-A*0207', 'HLA-A*0224', 'HLA-A*0301', 'HLA-A*0362', 'HLA-A*1101', 'HLA-A*2301', 'HLA-A*2402', 'HLA-A*3001', 'HLA-A*3003', 'HLA-A*6801', 'HLA-A*9234', 'HLA-A*9235', 'HLA-A*9253', 'HLA-B*0602', 'HLA-B*0702', 'HLA-B*0801', 'HLA-B*1402', 'HLA-B*1501', 'HLA-B*1557', 'HLA-B*1801', 'HLA-B*2703', 'HLA-B*2705', 'HLA-B*2709', 'HLA-B*2713', 'HLA-B*3501', 'HLA-B*3505', 'HLA-B*3508', 'HLA-B*3901', 'HLA-B*4001', 'HLA-B*4002', 'HLA-B*4044', 'HLA-B*4102', 'HLA-B*4104', 'HLA-B*4201', 'HLA-B*4202', 'HLA-B*4402', 'HLA-B*4403', 'HLA-B*4405', 'HLA-B*4601', 'HLA-B*5101', 'HLA-B*5301', 'HLA-B*5701', 'HLA-B*5703', 'HLA-B*5706', 'HLA-B*5712', 'HLA-B*5801', 'HLA-B*8102', 'HLA-B*8103', 'HLA-B*9234', 'HLA-C*0102', 'HLA-C*0304', 'HLA-C*0401', 'HLA-C*0517', 'HLA-C*0602', 'HLA-C*0756', 'HLA-C*1510', 'HLA-C*1604'] enum: - "HLA-A*0101" - "HLA-A*0201" - "HLA-A*0203" - "HLA-A*0205" - "HLA-A*0206" - "HLA-A*0207" - "HLA-A*0224" - "HLA-A*0301" - "HLA-A*0362" - "HLA-A*1101" - "HLA-A*2301" - "HLA-A*2402" - "HLA-A*3001" - "HLA-A*3003" - "HLA-A*6801" - "HLA-A*9234" - "HLA-A*9235" - "HLA-A*9253" - "HLA-B*0602" - "HLA-B*0702" - "HLA-B*0801" - "HLA-B*1402" - "HLA-B*1501" - "HLA-B*1557" - "HLA-B*1801" - "HLA-B*2703" - "HLA-B*2705" - "HLA-B*2709" - "HLA-B*2713" - "HLA-B*3501" - "HLA-B*3505" - "HLA-B*3508" - "HLA-B*3901" - "HLA-B*4001" - "HLA-B*4002" - "HLA-B*4044" - "HLA-B*4102" - "HLA-B*4104" - "HLA-B*4201" - "HLA-B*4202" - "HLA-B*4402" - "HLA-B*4403" - "HLA-B*4405" - "HLA-B*4601" - "HLA-B*5101" - "HLA-B*5301" - "HLA-B*5701" - "HLA-B*5703" - "HLA-B*5706" - "HLA-B*5712" - "HLA-B*5801" - "HLA-B*8102" - "HLA-B*8103" - "HLA-B*9234" - "HLA-C*0102" - "HLA-C*0304" - "HLA-C*0401" - "HLA-C*0517" - "HLA-C*0602" - "HLA-C*0756" - "HLA-C*1510" - "HLA-C*1604" # Deeprank-Ab Settings DeeprankAbSettings: type: object required: - task - pdbFile - heavyChain - lightChain - antigenChain properties: task: type: string description: "Choose antibody (heavy+light) or nanobody (single-chain binder)" default: "antibody" enum: - "antibody" - "nanobody" pdbFile: type: string description: "Antibody- or nanobody-antigen complex PDB file (single model or ensemble with multiple MODEL records) File with extensions [pdb]" example: {'antibody': '7DK2_AB_C.pdb', 'nanobody': '9f6o.pdb'} format: binary heavyChain: type: string description: "Binder chain ID in the complex PDB (heavy chain for antibody, single chain for nanobody)" example: {'antibody': 'A', 'nanobody': 'B'} lightChain: type: string description: "Light-chain ID in the complex PDB (required for antibody task) [Only available when task is one of antibody]" example: "B" antigenChain: type: string description: "Antigen chain ID in the complex PDB" example: {'antibody': 'C', 'nanobody': 'A'} # Deepsp Settings DeepspSettings: type: object required: - heavySequence - lightSequence properties: heavySequence: type: string description: "Heavy sequence of your antibody" example: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" lightSequence: type: string description: "Light sequence of your antibody" example: "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIN" # Deepstabp Settings DeepstabpSettings: type: object required: - sequence properties: sequence: type: string description: "Protein sequence to assess thermostability" example: "MAQYHQQHEMKQTMAETQYVTAPPPMGYPVMMKDSPQTVQPPHEGQSKGSGGFLRGCLAAMCCCCVLDCVF" growthTemp: type: number default: 22 measurementCondition: type: string description: "Protein environment" default: "cell" enum: - "cell" - "lysate" # Dfmdock Settings DfmdockSettings: type: object required: - receptorFile - ligandFile properties: receptorFile: type: string description: "PDB file for the receptor protein. File with extensions [pdb]" example: "1ACB_receptor.pdb" format: binary ligandFile: type: string description: "PDB file for the ligand protein. File with extensions [pdb]" example: "1ACB_ligand.pdb" format: binary numSamples: type: number description: "Number of docked poses to generate. More samples increases the chance of finding a high-quality pose." minimum: 1 maximum: 100 default: 10 # Diffdock Settings DiffdockSettings: type: object required: - proteinFile - ligandFormat - ligandFile - ligandSmiles properties: proteinFile: type: string description: "pdb structure file for your receptor File with extensions [pdb]" example: "6w70.pdb" format: binary ligandFormat: type: string description: "Choose the format of your ligand input" default: "sdf/mol2 file" enum: - "sdf/mol2 file" - "SMILES" ligandFile: type: string description: "sdf or mol2 structure file for your ligand File with extensions [sdf, mol2]" example: "6w70_ligand.sdf" format: binary ligandSmiles: type: string description: "SMILES string for your ligand" # Diffsbdd Settings DiffsbddSettings: type: object required: - task - proteinFile - ligandFile - fragmentsFile properties: task: type: string default: "generate" enum: - "optimize" - "generate" - "inpaint" proteinFile: type: string description: "pdb structure file for your receptor File with extensions [pdb]" example: "5ndu.pdb" format: binary ligandFile: type: string description: "sdf structure file for your ligand File with extensions [sdf] [Only available when task is one of optimize, inpaint, generate]" example: "5ndu_C_8V2.sdf" format: binary fragmentsFile: type: string description: "sdf structure file to define fixed substructures in your ligand File with extensions [sdf] [Only available when task is one of inpaint]" example: "fragments.sdf" format: binary centerLigand: type: boolean description: "Sample the additional atoms near the center of mass of the fixed substructure [Only available when task is one of inpaint]" default: False numSamples: type: number default: 20 numBatches: type: integer description: "Number of batches to design, each will have the # of samples you set in numSamples" default: 1 addNNodes: type: number description: "Random by default [Only available when task is one of inpaint]" relax: type: boolean default: False sanitize: type: boolean default: False resamplings: type: number default: 10 timesteps: type: number default: 100 saveTraj: type: boolean default: False # Disco Settings DiscoSettings: type: object required: - task - proteinLengthMin - proteinLengthMax - ligandInputType - ligandSmiles - ligandFile - ligandCcd - dnaSequence - rnaSequence - inputJson - experiment - effort properties: task: type: string default: "unconditional" enum: - "unconditional" - "ligand-conditioned" - "dna-conditioned" - "rna-conditioned" - "json" proteinLengthMin: type: number description: "Minimum number of residues. When Min < Max, each design samples a random length in [Min, Max]. [Only available when task is one of unconditional, ligand-conditioned, dna-conditioned, rna-conditioned]" example: {'ligand-conditioned': 150, 'dna-conditioned': 100, 'unconditional': 100, 'rna-conditioned': 100} minimum: 1 maximum: 800 default: 100 proteinLengthMax: type: number description: "Maximum number of residues. Set equal to Min for a fixed length. [Only available when task is one of unconditional, ligand-conditioned, dna-conditioned, rna-conditioned]" example: {'ligand-conditioned': 300, 'dna-conditioned': 200, 'unconditional': 200, 'rna-conditioned': 200} minimum: 1 maximum: 800 default: 200 partialSequence: type: string description: "Optionally specify fixed residues. Use standard amino acid letters for fixed positions and '-' for positions to design. Overrides Protein Length when provided. [Only available when task is one of unconditional, ligand-conditioned, dna-conditioned, rna-conditioned]" example: {'unconditional': '', 'ligand-conditioned': 'MKTL--------VPEG'} ligandInputType: type: string description: "How to specify the ligand [Only available when task is one of ligand-conditioned]" default: "smiles" enum: - "smiles" - "sdf" - "ccd" ligandSmiles: type: string description: "SMILES string for the target ligand [Only available when task is one of ligand-conditioned]" example: {'ligand-conditioned': 'CC(=O)Oc1ccccc1C(=O)O'} ligandFile: type: string description: "SDF, MOL, or MOL2 file with 3D coordinates for the target ligand File with extensions [sdf, mol, mol2] [Only available when task is one of ligand-conditioned]" format: binary ligandCcd: type: string description: "PDB Chemical Component Dictionary code. For multi-component ligands, separate codes with underscores (e.g., NAG_BMA_BGC) [Only available when task is one of ligand-conditioned]" example: {'ligand-conditioned': 'ATP'} dnaSequence: type: string description: "DNA sequence (5' to 3'). Use letters A, T, G, C only. [Only available when task is one of dna-conditioned]" example: {'dna-conditioned': 'GATTACAGATC'} doubleStranded: type: boolean description: "Automatically add the reverse complement as a second strand. Uncheck for single-stranded DNA. [Only available when task is one of dna-conditioned]" default: True rnaSequence: type: string description: "RNA sequence. Use letters A, U, G, C only. [Only available when task is one of rna-conditioned]" example: {'rna-conditioned': 'GGCUAGCCAUUUGAC'} inputJson: type: string description: "Full DISCO input JSON. Must be a JSON array. See DISCO docs for format: sequences with proteinChain, ligand, dnaSequence, rnaSequence, ion, and optional covalent_bonds. [Only available when task is one of json]" example: {'json': '[{"name": "my_design", "sequences": [{"proteinChain": {"sequence": "----------", "count": 1}}]}]'} experiment: type: string description: "Controls quality vs diversity trade-off. 'Designable' uses noisy guidance for higher confidence designs. 'Diverse' samples more freely for greater structural variety." default: {'ligand-conditioned': 'diverse', 'dna-conditioned': 'diverse', 'json': 'designable', 'unconditional': 'designable', 'rna-conditioned': 'diverse'} enum: - "designable" - "diverse" effort: type: string description: "Compute preset. 'Max' (200 steps, 4 cycles) for full quality. 'Fast' (100 steps, 2 cycles) is ~4x faster but ~10% lower quality. Only use 'fast' for unconditional generation." default: {'ligand-conditioned': 'max', 'dna-conditioned': 'max', 'json': 'max', 'unconditional': 'fast', 'rna-conditioned': 'max'} enum: - "max" - "fast" numDesigns: type: integer description: "Number of designs to generate (each runs as a separate job with a random seed)" default: 1 # Dlkcat Settings DlkcatSettings: type: object required: - sequence - smiles properties: sequence: type: string description: "Enzyme sequence to assess kcat" example: "MVHVRKNHLTMTAEEKRRFVHAVLEIKRRGIYDRFVKLHIQINSTDYLDKETGKRLGHVNPGFLPWHRQYLLKFEQALQKVDPRVTLPYWDWTTDHGENSPLWSDTFMGGNGRPGDRRVMTGPFARRNGWKLNISVIPEGPEDPALNGNYTHDDRDYLVRDFGTLTPDLPTPQELEQTLDLTVYDCPPWNHTSGGTPPYESFRNHLEGYTKFAWEPRLGKLHGAAHVWTGGHMMYIGSPNDPVFFLNHCMIDRCWALWQARHPDVPHYLPTVPTQDVPDLNTPLGPWHTKTPADLLDHTRFYTYDQ" smiles: type: string example: "C1=CC=C(C(=C1)O)O" # Dnaworks Settings DnaworksSettings: type: object required: - inputType - seq properties: inputType: type: string description: "Choose between nucleotide or protein sequence input" enum: - "nucleotide" - "protein" seq: type: string example: "MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFGYGL" maxLength: 5000 expressionHost: type: string description: "Codon optimization is performed for this organism (only applies to protein input)" enum: - "ecoli2" - "E. coli" - "C. elegans" - "D. melanogaster" - "H. sapiens" - "M. musculus" - "R. novegicus" - "S. cerevesiae" - "X. laevis" - "P. pastoris" tbio: type: boolean description: "Enable thermodynamically balanced inside-out gene synthesis strategy" default: False nogaps: type: boolean description: "Avoid inserting gaps between oligos by minimizing overlap spacing" default: False solutions: type: number description: "Generate multiple alternative oligo designs" minimum: 1 maximum: 10 default: 1 melting: type: number description: "Melting temperature for overlapping oligo regions" minimum: 55 maximum: 75 default: 65 length: type: number description: "Target length for each designed oligo" minimum: 0 maximum: 60 default: 40 reverse: type: boolean description: "Reverse-complement the input sequence before processing" default: False gapfix: type: boolean description: "Force input sequence to fall in non-overlapping regions (useful for mutation insertion)" default: False # Dockq Settings DockqSettings: type: object required: - modelFile - nativeFile properties: modelFile: type: string description: "Model pdb structure File with extensions [pdb]" format: binary nativeFile: type: string description: "Native pdb structure File with extensions [pdb]" format: binary allowedMismatches: type: number description: "Number of allowed mismatches when mapping model sequence to native sequence" default: 0 # Drugflow Settings DrugflowSettings: type: object required: - pdbFile - referenceLigandFile - numSamples - numBatches - distCutoff properties: pdbFile: type: string description: "pdb structure file for your receptor File with extensions [pdb]" example: "6w70.pdb" format: binary referenceLigandFile: type: string description: "sdf structure file for your ligand File with extensions [sdf]" example: "6w70_ligand.sdf" format: binary numSamples: type: number default: 10 numBatches: type: integer description: "Number of batches, each with the chosen number of samples" default: 1 molSize: type: array items: type: string description: "Maximum number/range of atoms - Can be a single number or a range. Leave empty for size to be sampled." example: ["15", "20"] minimum: 0 nSteps: type: number description: "Number of denoising steps - Leave empty for None" distCutoff: type: number description: "Distance to define the pocket around the reference ligand" minimum: 5 default: 8 # Dsmbind Settings DsmbindSettings: type: object required: - binderPdb - binderChain - targetPdb - targetChain properties: binderPdb: type: string example: "9f6o.pdb" format: binary binderChain: type: string example: "B" targetPdb: type: string example: "9f6o.pdb" format: binary targetChain: type: string example: "A" # Electronic-Properties Settings ElectronicPropertiesSettings: type: object required: - inputType - smiles - sdfFile - xyzFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" - "xyz" smiles: type: string description: "SMILES string of the molecule [Only available when inputType is one of smiles]" example: "c1ccccc1" sdfFile: type: string description: "SDF/MOL file with 3D coordinates File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary xyzFile: type: string description: "XYZ coordinate file (e.g. from geometry optimization) File with extensions [xyz] [Only available when inputType is one of xyz]" format: binary method: type: string description: "Level of theory. Performs three calculations (neutral, cation, anion) to compute all properties. g-xTB: gas-phase only" default: "b3lyp" enum: - "xtb-gfn2" - "g-xtb" - "b3lyp" - "wb97x-d3" basisSet: type: string description: "Basis set for DFT methods. Use -d (diffuse) variants for anions" default: "def2-svp" enum: - "def2-svp" - "def2-svpd" - "def2-tzvp" - "def2-tzvpd" - "6-31g*" charge: type: number description: "Net molecular charge of the neutral (reference) state" default: 0 multiplicity: type: number description: "Spin multiplicity (2S+1) of the neutral state" default: 1 solvent: type: string description: "Implicit solvation environment" default: "none" enum: - "none" - "water" - "acetonitrile" - "dmso" - "methanol" - "ethanol" - "chloroform" - "toluene" - "thf" - "dichloromethane" preOptimize: type: boolean description: "Run a fast xTB geometry optimization first. Recommended for SMILES input" default: True # Electrostatic-Potential Settings ElectrostaticPotentialSettings: type: object required: - inputType - smiles - sdfFile - xyzFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" - "xyz" smiles: type: string description: "SMILES string of the molecule [Only available when inputType is one of smiles]" example: "CC(=O)O" sdfFile: type: string description: "SDF/MOL file with 3D coordinates File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary xyzFile: type: string description: "XYZ coordinate file (e.g. from geometry optimization) File with extensions [xyz] [Only available when inputType is one of xyz]" format: binary method: type: string description: "Level of theory for computing the electrostatic potential" default: "xtb-gfn2" enum: - "xtb-gfn2" - "b3lyp" - "hf" basisSet: type: string description: "Basis set for DFT/HF methods" default: "def2-svp" enum: - "def2-svp" - "def2-svpd" - "def2-tzvp" - "def2-tzvpd" charge: type: number description: "Net molecular charge" default: 0 multiplicity: type: number description: "Spin multiplicity (2S+1)" default: 1 solvent: type: string description: "Implicit solvation environment" default: "none" enum: - "none" - "water" - "acetonitrile" - "dmso" - "methanol" - "ethanol" - "chloroform" - "toluene" - "thf" - "dichloromethane" surfaceType: type: string description: "Surface on which to compute the potential. vdw: van der Waals surface" default: "vdw" enum: - "vdw" gridDensity: type: string description: "Resolution of the surface grid. Fine gives smoother results but takes longer" default: "medium" enum: - "coarse" - "medium" - "fine" preOptimize: type: boolean description: "Run a fast xTB geometry optimization first. Recommended for SMILES input" default: True # Emboss Settings EmbossSettings: type: object required: - sequence - organism properties: sequence: type: string example: "MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFGYGL" maxLength: 5000 organism: type: string default: "Ehum" enum: - "Ehum" - "Eyeast_high" # Enumeration Settings EnumerationSettings: type: object required: - scaffoldSmiles - rgroupFile properties: scaffoldSmiles: type: string description: "Scaffold with R-group positions marked as [*:1], [*:2], etc. Example: c1ccc([*:1])cc1[*:2]" example: "c1ccc([*:1])cc1[*:2]" rgroupFile: type: string description: "CSV with one column per R-group position (columns can have different lengths). Use [*] to mark attachment atom for multi-atom fragments (e.g. [*]c1ccc(O)cc1 for para-phenol). Single atoms (C, N, Cl, etc.) don't need [*]. If no [*] is specified, the first atom is used as the attachment point. File with extensions [csv]" format: binary rgroupColumns: type: string description: "Column names in position order, e.g. Amines,Acids maps to [*:1],[*:2]. Leave blank to auto-detect R1,R2,R3,... columns" maxEnumerated: type: number description: "Maximum number of output molecules. For large combinatorial spaces (>100k), random sampling is used automatically" default: 1000 diversitySelect: type: number description: "Select N most diverse molecules using MaxMin fingerprint picking (0 = return all)" default: 0 deduplicate: type: boolean description: "Remove duplicate canonical SMILES from the output" default: True filterLipinski: type: boolean description: "Discard molecules violating Lipinski Rule of 5 (MW > 500, LogP > 5, HBD > 5, HBA > 10)" default: False maxMW: type: number description: "Discard molecules above this MW (0 = no limit)" default: 0 maxLogP: type: number description: "Discard molecules above this LogP (0 = no limit)" default: 0 maxTPSA: type: number description: "Discard molecules above this topological polar surface area in A² (0 = no limit)" default: 0 maxRotatable: type: number description: "Discard molecules with more rotatable bonds than this (0 = no limit)" default: 0 # Enzygen2 Settings Enzygen2Settings: type: object required: - pdbFile - chain - motif - ncbiId - numDesigns properties: pdbFile: type: string description: "PDB or CIF file of the reference enzyme structure File with extensions [pdb]" example: "3DWZ.pdb" format: binary chain: type: string description: "Chain to use for enzyme design" example: "A" motif: type: string description: "Functionally important residue positions to keep fixed during design (active site, catalytic residues, etc.)" example: "49,51,52,57,58,59,60,61,66,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,90,92,93,94,95,97,103,107,109,113,118,119,120,121,123,124,125,126,127,128,129,130,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,168,169,172,173,175,177,178,179,182,183,184,185,186,190,191,192,193,194,195,196,197,198,199,203,206,209,211,212,213,214,215,220,221,222,223,224,225,226,227,230,231,232,233,237,238,239,240,242,243,245,247,249,250,251,252,254,256,257,260,261,262,263,264,265,266,272,274,277,281,288,289,294,295,296,297,298,299" ncbiId: type: string description: "NCBI taxonomic identifier for the target organism (e.g. 83332 for Mycobacterium tuberculosis, 562 for E. coli)" example: "83332" numDesigns: type: integer description: "Number of enzyme variants to generate" default: 1 decodingStrategy: type: string description: "Sampling strategy for sequence generation" default: "top-p" enum: - "greedy" - "top-k" - "top-p" toppProbability: type: number description: "Cumulative probability threshold for nucleus sampling (lower = more conservative)" minimum: 0.01 maximum: 1 default: 0.2 # Enzygen2-Finetune Settings Enzygen2FinetuneSettings: type: object required: - dataFile - proteinTask properties: dataFile: type: string description: "EnzyGen2-format JSON file keyed by NCBI taxonomy IDs, each containing train/valid splits with sequences, C-alpha coordinates, and motif indices. All keys in the file are used for training. File with extensions [json]" example: "enzygen2_example_finetune.json" format: binary proteinTask: type: string description: "An NCBI taxonomy ID present in your JSON file. Used as the primary taxonomy embedding for the finetuned model (e.g. '77133'). The JSON may contain multiple keys — all are used for training." example: "77133" epochs: type: number description: "Maximum number of training epochs" minimum: 1 maximum: 200 default: 50 learningRate: type: number default: 5e-05 maxUpdate: type: number default: 300000 dropout: type: number description: "Dropout rate during training (0.0 to 1.0)" default: 0.3 # Enzygen2-Inference Settings Enzygen2InferenceSettings: type: object required: - pdbFile - chain - motif - ncbiId - numDesigns properties: pdbFile: type: string description: "PDB or CIF file of the reference enzyme structure File with extensions [pdb]" example: "3DWZ.pdb" format: binary chain: type: string description: "Chain to use for enzyme design" example: "A" motif: type: string description: "Functionally important residue positions to keep fixed during design (active site, catalytic residues, etc.)" example: "49,51,52,57,58,59,60,61,66,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,90,92,93,94,95,97,103,107,109,113,118,119,120,121,123,124,125,126,127,128,129,130,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,168,169,172,173,175,177,178,179,182,183,184,185,186,190,191,192,193,194,195,196,197,198,199,203,206,209,211,212,213,214,215,220,221,222,223,224,225,226,227,230,231,232,233,237,238,239,240,242,243,245,247,249,250,251,252,254,256,257,260,261,262,263,264,265,266,272,274,277,281,288,289,294,295,296,297,298,299" ncbiId: type: string description: "NCBI taxonomic identifier for the target organism (e.g. 83332 for Mycobacterium tuberculosis, 562 for E. coli)" example: "83332" numDesigns: type: integer description: "Number of enzyme variants to generate" default: 1 decodingStrategy: type: string description: "Sampling strategy for sequence generation" default: "top-p" enum: - "greedy" - "top-k" - "top-p" toppProbability: type: number description: "Cumulative probability threshold for nucleus sampling (lower = more conservative)" minimum: 0.01 maximum: 1 default: 0.4 # Equidock Settings EquidockSettings: type: object required: - receptorFile - ligandFile properties: receptorFile: type: string description: "pdb structure file for your receptor File with extensions [pdb]" format: binary ligandFile: type: string description: "pdb structure file for your ligand File with extensions [pdb]" format: binary # Esm-Embeddings Settings EsmEmbeddingsSettings: type: object required: - sequence properties: model: type: string description: "Model size to use for embeddings" default: "esm2_t33_650M_UR50D" enum: - "esm2_t6_8M_UR50D" - "esm2_t12_35M_UR50D" - "esm2_t30_150M_UR50D" - "esm2_t33_650M_UR50D" - "esm2_t36_3B_UR50D" - "esm2_t48_15B_UR50D" sequence: type: string description: "Sequence to compute embedding" example: "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIN" outputFormat: type: string description: "Format to save embeddings in" default: "pt" enum: - "pt" - "json" sequenceBatching: type: boolean description: "Batch process the input sequences" default: False sequenceBatchSize: type: number description: "Determines the number of sequences in each batch" # Esm-If1 Settings EsmIf1Settings: type: object required: - pdbFile - chain - designedResidues properties: pdbFile: type: string description: "Protein structure file to be designed (Please make sure that the indices are numbered from 1 to N) File with extensions [pdb]" example: "3htn_renum.pdb" format: binary chain: type: string description: "Chain ID to be designed" example: "A" designedResidues: type: string example: "62-70" numSequences: type: number description: "Number of sequences to be generated for the protein backbone" default: 10 # Esm-Scan Settings EsmScanSettings: type: object required: - sequence properties: sequence: type: string description: "Sequence to score point mutations" example: "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIN" # Esm2 Settings Esm2Settings: type: object required: - task - sequence - maskedResidues properties: task: type: string default: "mask" enum: - "mask" - "scan" sequence: type: string example: "EVQLVQSGPEVKKPGTSVKVSCKASGFTFMSSAVQWVRQARGQRLEWIGWIVIGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSSISCNDGFDIWGQGTMVTVS" maskedResidues: type: string example: "25 26 27 28 29 30 31 32" # Esmfold Settings EsmfoldSettings: type: object required: - sequence properties: sequence: type: string description: "Protein amino acid sequence, place a : between chains for multimers" example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" # Evcouplings Settings EvcouplingsSettings: type: object required: - sequence properties: sequence: type: string description: "Protein amino acid sequence" example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" maxLength: 5000 # Evo2 Settings Evo2Settings: type: object required: - task - sequence - seed properties: task: type: string default: "generate" enum: - "generate" - "embeddings" model: type: string description: "Parameter scale of the Evo 2 model" default: "7b" enum: - "7b" - "20b" - "40b" embeddingLayer: type: string description: "Model layer to extract embeddings from [Only available when task is one of embeddings]" default: "blocks.28.mlp.l3" sequence: type: string description: "DNA sequence for which to calculate embeddings [Only available when task is one of embeddings]" example: "ATGAGCGATATCGCTCTGGTGATGAACGAATTCCAGGCGCTGGGGCTGACCGACAAACCTGCCGATCTGGCAGATATCGCGCGCGTGAAAGAGATGAAAGAGGCCGAAGCCCGCGAACGCATT" seed: type: string description: "DNA seed sequence to prompt the model for generation [Only available when task is one of generate]" example: "ATGAGCGATATCGCTCTGGTGATGAACGAATTCCAGGCGCTGGGGCTGACCGACAAACCTGCCGATCTGGCAGATATCGCGCGCGTGAAAGAGATGAAAGAGGCCGAAGCCCGCGAACGCATT" length: type: number description: "Number of tokens (nucleotides) to generate [Only available when task is one of generate]" default: 200 numSequences: type: number description: "Number of sequences to generate [Only available when task is one of generate]" default: 10 temperature: type: number description: "Controls randomness of generation. Higher values produce more diverse sequences. [Only available when task is one of generate]" default: 1 topK: type: number description: "Limits sampling to the top K most likely tokens at each step [Only available when task is one of generate]" default: 4 topP: type: number description: "Nucleus sampling threshold. Limits sampling to tokens with cumulative probability up to this value. [Only available when task is one of generate]" default: 1 # Evonb Settings EvonbSettings: type: object required: - sequence properties: sequence: type: string description: "Sequence" example: "QVQLVESGGGLVQSGGSLRLSCAASGSIFRTTGMNWYRQTPEKQREWVALITSHGTTSYAASVEGRFTISRDSAGTTVYLQMNSLKPEDAGVYYCTTRGYWGQGTQVTVSS" # Evopro Settings EvoproSettings: type: object required: - receptorSequence - binderSequence - binderDesignedResidues - receptorContactResidues properties: receptorSequence: type: string example: "WNPPTFSPALLVVTEGDNATFTCSFSNTSESFHVVWHRESPSGQTDTLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYVCGVISLAPKIQIKESLRAELRVTERRAE" binderSequence: type: string example: "DEKEELLRELQEKIPDPRVREVLELAIKLLEDGVPPEEIKKLIEKLVKELGLPPEVLELVEKIVK" binderDesignedResidues: type: string example: "B1-B65" receptorContactResidues: type: string example: "A31-A58,A88-A108" # Evoprotgrad Settings EvoprotgradSettings: type: object required: - sequence properties: sequence: type: string description: "Amino acid sequence to be mutated" example: "KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEG" numDesigns: type: integer description: "Number of designs to generate" default: 1 maxMutations: type: number description: "Maximum number of mutations in a design" default: 10 numSteps: type: number description: "Number of steps to evolve the protein for" default: 20 # Fampnn Settings FampnnSettings: type: object required: - pdbFile - chains properties: pdbFile: type: string description: "Protein structure file to design with FAMPNN File with extensions [pdb]" example: "9f6o.pdb" format: binary numSamples: type: number description: "Number of designed sequences and packed structures to generate for each input backbone" minimum: 1 maximum: 1000 default: 2 temperature: type: number description: "Sampling temperature for sequence design. Higher values increase diversity." minimum: 0 maximum: 1 default: 0.1 samplingSteps: type: number description: "Number of FAMPNN sequence denoising steps to run during design" minimum: 1 maximum: 200 default: 100 chains: type: array items: type: string description: "Select the input PDB chains to include in FAMPNN design. Fixed residue selections below only apply to these chains." example: ["A"] fixedSequenceResidues: type: object description: "Optional chain-aware residues to keep fixed during design" example: {'A': '165-190 200-210'} default: {} fixedSidechainResidues: type: object description: "Optional chain-aware residues whose input sidechains should be preserved. These positions must be a subset of Fixed Sequence Residues." example: {'A': '170-180'} default: {} # Fastsolv Settings FastsolvSettings: type: object required: - solventSmiles - soluteSmiles properties: solventSmiles: type: string example: "CO" soluteSmiles: type: string example: "CC(=O)Nc1ccc(O)cc1" temperature: type: number default: 298 # File-Converter Settings FileConverterSettings: type: object required: - inputFileType - pdbFile - cifFile - sdfFile - smilesStrings properties: inputFileType: type: string default: "pdb" enum: - "pdb" - "cif" - "sdf" - "smiles" pdbFile: type: string description: "PDB file to convert to CIF File with extensions [pdb] [Only available when inputFileType is one of pdb]" format: binary cifFile: type: string description: "CIF file to convert to PDB File with extensions [cif] [Only available when inputFileType is one of cif]" format: binary sdfFile: type: string description: "SDF file to convert to SMILES File with extensions [sdf] [Only available when inputFileType is one of sdf]" format: binary smilesStrings: type: string description: "SMILES strings to conver to SDF [Only available when inputFileType is one of smiles]" default: [] # Fixbb Settings FixbbSettings: type: object required: - pdbFile - chain - numDesigns properties: pdbFile: type: string description: "Protein structure in pdb format, should be File with extensions [pdb]" example: "1haz.pdb" format: binary chain: type: string example: "B" designedResidues: type: string description: "Residues to design in the original pdb" example: "26-32" numDesigns: type: integer description: "Number of sequences to produce" default: 1 numRecycles: type: number description: "Number of times to recycle outputs back through structure prediction process for refined results" minimum: 0 maximum: 20 default: "0" dropout: type: boolean default: True recycle_mode: type: string description: "\"last\" - use loss from last recycle, \"average\" - compute and average at each recycle, \"sample\" - same as last, different # iterations each time, \"first\" - use first recycle, \"add_prev\" - average outputs, \"backprop\" - backprop through recycles" default: "last" enum: - "last" - "average" - "sample" - "first" - "add_prev" - "backprop" useTemplates: type: boolean description: "Enable template structure usage for improved predictions" default: False enableTemplateMasking: type: boolean description: "Apply selective template masking to allow free design in unfixed regions while maintaining structural anchors in fixed regions" default: False # Flowdock Settings FlowdockSettings: type: object required: - pdbFile - sequence - smiles properties: pdbFile: type: string format: binary sequence: type: string description: "Protein sequence input, with chains separated by \":\"" smiles: type: string # Foldmason Settings FoldmasonSettings: type: object required: - proteinFiles properties: proteinFiles: type: string description: "Pdb/cif files or zip file containing pdb/cif files to align File with extensions [pdb, cif, zip]" format: binary # Foldseek Settings FoldseekSettings: type: object required: - task - database - pdbFile - fastaFile - customSearchDbFiles - customFastaDbFiles - proteinFiles properties: task: type: string description: "Search or cluster structures" default: "search" enum: - "search" - "cluster" database: type: string description: "Database to search against [Only available when task is one of search]" default: "pdb" enum: - "pdb" - "alphafold-uniprot" - "alphafold-uniprot50" - "alphafold-swiss-prot" - "alphafold-proteome" - "esmatlas30" - "custom" - "custom-fasta" pdbFile: type: string description: "Protein structure file to search with File with extensions [pdb] [Only available when task is one of search]" format: binary fastaFile: type: string description: "Protein sequence file to search with (uses ProstT5 for 3Di prediction) File with extensions [fasta, fa] [Only available when task is one of search]" format: binary multimer: type: boolean default: False customSearchDbFiles: type: string description: "Pdb files or zip file containing pdb files to search File with extensions [pdb, zip, /, *]" format: binary customFastaDbFiles: type: string description: "FASTA files containing protein sequences to create a custom database using ProstT5 for 3Di prediction. Creates a structural database directly from sequences without requiring PDB structures. File with extensions [fasta, fa, zip, /, *]" format: binary proteinFiles: type: string description: "Pdb files or zip file containing pdb files to cluster File with extensions [pdb, zip] [Only available when task is one of cluster]" format: binary customOutputColumns: type: boolean description: "Choose specific output columns (default columns used if unchecked) [Only available when task is one of search]" default: False outputColumns: type: string description: "Select specific output columns for the results [Only available when task is one of search]" enum: - "query" - "target" - "evalue" - "pident" - "fident" - "alnlen" - "mismatch" - "gapopen" - "qstart" - "qend" - "tstart" - "tend" - "qlen" - "tlen" - "bits" - "qcov" - "tcov" - "qseq" - "tseq" - "qaln" - "taln" - "qheader" - "theader" - "qframe" - "tframe" - "cigar" - "qset" - "tset" - "tsetid" - "empty" - "qca" - "tca" - "alntmscore" - "qtmscore" - "ttmscore" - "u" - "t" - "lddt" - "lddtfull" - "prob" outputColumnsMultimer: type: string description: "Select specific output columns for the results [Only available when task is one of search]" enum: - "query" - "target" - "evalue" - "pident" - "fident" - "alnlen" - "mismatch" - "gapopen" - "qstart" - "qend" - "tstart" - "tend" - "qlen" - "tlen" - "bits" - "qcov" - "tcov" - "qseq" - "tseq" - "qaln" - "taln" - "qheader" - "theader" - "qframe" - "tframe" - "cigar" - "qset" - "tset" - "tsetid" - "empty" - "qca" - "tca" - "alntmscore" - "qtmscore" - "ttmscore" - "u" - "t" - "lddt" - "lddtfull" - "prob" - "complexqtmscore" - "complexttmscore" - "complexu" - "complext" - "qcomplexcoverage" - "tcomplexcoverage" - "qchaintms" - "tchaintms" - "qchains" - "tchains" - "interfacelddt" - "complexassignid" sensitivityToSpeed: type: number description: "Adjust sensitivity to speed trade-off; lower is faster, higher more sensitive [Only available when task is one of search]" minimum: 4 maximum: 15 default: 9.5 maxSeqs: type: number description: "Adjust the amount of prefilter handed to alignment; increasing it can lead to more hits [Only available when task is one of search]" minimum: 100 maximum: 10000 default: 1000 evalue: type: number description: "List matches below this E-value; increasing it reports more distant structures [Only available when task is one of search]" minimum: 0 default: 0.001 alignmentType: type: string description: "How to compute alignment [Only available when task is one of search]" default: "2" enum: - "0" - "1" - "2" coverage: type: number description: "List matches above this fraction of aligned (covered) residues; higher coverage = more global alignment [Only available when task is one of search]" minimum: 0 maximum: 1 default: 0 # Fpocket Settings FpocketSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein to identify pocket on File with extensions [pdb]" example: "4N0Y_receptor_1.pdb" format: binary # Frameflow Settings FrameflowSettings: type: object required: - pdbFile - contigs - chain properties: pdbFile: type: string description: "Pdb structure file to scaffold File with extensions [pdb]" example: "3HTN.pdb" format: binary contigs: type: string description: "String describing fixed and variable regions of protein, see https://www.tamarind.bio/frameflow to generate contigs for your task" example: "10-40,A100-120,10-40" chain: type: string description: "Chain to design" example: "A" numDesigns: type: number description: "Number of designs to generate (1-16)" default: 1 # Frequency-Analysis Settings FrequencyAnalysisSettings: type: object required: - inputType - smiles - sdfFile - xyzFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" - "xyz" smiles: type: string description: "SMILES string of the molecule [Only available when inputType is one of smiles]" example: "CCO" sdfFile: type: string description: "SDF/MOL file with 3D coordinates File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary xyzFile: type: string description: "Pre-optimized XYZ file (recommended: use output from geometry optimization) File with extensions [xyz] [Only available when inputType is one of xyz]" format: binary method: type: string description: "xtb-gfn2: fast semiempirical (~10s). r2scan-3c: composite DFT (~3min). b3lyp/wb97x-d3: full DFT (~10-30min)" default: "xtb-gfn2" enum: - "xtb-gfn2" - "r2scan-3c" - "b3lyp" - "wb97x-d3" basisSet: type: string description: "Basis set for DFT methods. Use -d (diffuse) variants for anions" default: "def2-svp" enum: - "def2-svp" - "def2-svpd" - "def2-tzvp" - "def2-tzvpd" - "6-31g*" charge: type: number description: "Net molecular charge" default: 0 multiplicity: type: number description: "Spin multiplicity (2S+1)" default: 1 solvent: type: string description: "Implicit solvation environment" default: "none" enum: - "none" - "water" - "acetonitrile" - "dmso" - "methanol" - "ethanol" - "chloroform" - "toluene" - "thf" - "dichloromethane" temperature: type: number description: "Temperature for thermochemical corrections (default 298.15 K = 25 C)" default: 298.15 pressure: type: number description: "Pressure for thermochemical corrections (default 1 atm)" default: 1 scaleFrequencies: type: number description: "Empirical scaling factor for computed frequencies (e.g. 0.9614 for B3LYP/6-31G*). 1.0 = no scaling" default: 1 preOptimize: type: boolean description: "Run geometry optimization before frequency analysis. Recommended unless input is already optimized" default: True # Fukui Settings FukuiSettings: type: object required: - inputType - smiles - sdfFile - xyzFile properties: inputType: type: string description: "Type of input to use File with extensions [sdf]" default: "smiles" enum: - "smiles" - "sdf" - "xyz" smiles: type: string example: "CC(=O)c1ccc(O)cc1" sdfFile: type: string example: "c1cc(O)ccc1C(=O)C (Neutral Structure).sdf" format: binary xyzFile: type: string format: binary charge: type: number description: "Charge of the molecule" default: 0 pcmWater: type: boolean description: "Enable implicit water solvation using PCM model for more realistic aqueous environment calculations" default: False # G-Mmpbsa Settings GMmpbsaSettings: type: object required: - topologyFile - trajectoryFile - groupDefinition - indexFile - receptorGroup - ligandGroup - receptorSelection - ligandSelection properties: topologyFile: type: string description: "GROMACS run input file containing topology and simulation parameters File with extensions [tpr]" format: binary trajectoryFile: type: string description: "Trajectory file from your MD simulation File with extensions [xtc]" format: binary groupDefinition: type: string default: "index-file" enum: - "index-file" - "specify-groups" indexFile: type: string description: "Index file defining group names for receptor and ligand File with extensions [ndx] [Only available when groupDefinition is one of index-file]" format: binary receptorGroup: type: string description: "Group name in index file corresponding to the receptor [Only available when groupDefinition is one of index-file]" example: "Protein" ligandGroup: type: string description: "Group name in index file corresponding to the ligand [Only available when groupDefinition is one of index-file]" example: "BEC" receptorSelection: type: string description: "Define receptor by residue ranges only. Format: '1-100' or '1-50,60-120' for multiple ranges. [Only available when groupDefinition is one of specify-groups]" example: "1-250" ligandSelection: type: string description: "Define ligand by residue ranges only. Format: '300-350' or multiple ranges separated by commas. [Only available when groupDefinition is one of specify-groups]" example: "300-350" proteinDielectric: type: number description: "Dielectric constant used in Poisson–Boltzmann calculations" default: 2 # Gbsa Settings GbsaSettings: type: object required: - task - proteinFile - ligandFile - complexFile - receptorChains - binderChains - method - mode properties: task: type: string default: "protein-ligand" enum: - "protein-ligand" - "protein-protein" proteinFile: type: string example: "6w70.pdb" format: binary ligandFile: type: string description: "Ligand SDF or MOL2 file File with extensions [sdf, mol2] [Only available when task is one of protein-ligand]" example: "6w70_ligand.sdf" format: binary complexFile: type: string description: "PDB file containing the protein-protein complex File with extensions [pdb] [Only available when task is one of protein-protein]" format: binary receptorChains: type: array items: type: string description: "Chain IDs of the receptor protein [Only available when task is one of protein-protein]" example: ["A"] binderChains: type: array items: type: string description: "Chain IDs of the binder protein [Only available when task is one of protein-protein]" example: ["B"] method: type: string description: "Solvation model for binding free energy calculation" default: "gb" enum: - "gb" - "pb" mode: type: string description: "Energy minimization uses the input pose directly. MD runs a full molecular dynamics simulation." default: "em" enum: - "em" - "md" nsteps: type: number description: "Number of MD simulation steps" default: 500000 eqsteps: type: number description: "Number of equilibration (NVT/NPT) steps before production MD" default: 50000 nframe: type: number description: "Number of trajectory frames to save and score" default: 100 # Gems Settings GemsSettings: type: object required: - pdbFile - sdfFile properties: pdbFile: type: string description: "PDB file containing the protein structure File with extensions [pdb]" example: "1a30.pdb" format: binary sdfFile: type: string description: "SDF file containing the bound ligand 3D structure File with extensions [sdf]" example: "1a30.sdf" format: binary # Geometry-Optimization Settings GeometryOptimizationSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "Type of input to use File with extensions [sdf]" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string example: "CC(=O)c1ccc(O)cc1" sdfFile: type: string example: "c1cc(O)ccc1C(=O)C (Neutral Structure).sdf" format: binary # Germinal Settings GerminalSettings: type: object required: - task - targetPdb - targetChain - binderPdb - binderChain - cdrLengths - fwLengths - vhFirst - vhLen - vlLen properties: task: type: string default: "VHH" enum: - "VHH" - "scFv" targetPdb: type: string description: "Protein structure of your target File with extensions [pdb]" example: "pdl1_germinal.pdb" format: binary targetChain: type: string description: "Target chain to design a binder to" example: "A" hotspotResidues: type: string description: "Specify hotspot residues on your target protein for the VHH/scFv binder to focus on during design. Enter residue numbers separated by commas (e.g., 305,456)." example: "37,39,41,96,98" default: "" framework: type: string description: "Choose from generic nanobody/scfv frameworks from Germinal paper or upload your own" example: {'scFv': 'generic', 'VHH': 'generic'} default: {'scFv': 'generic', 'VHH': 'generic'} enum: - "generic" - "custom" binderPdb: type: string description: "Antibody framework that we wish to use for our design. Germinal will only design the structure and sequence of regions of the framework which are annotated as CDRs. This structure does not have to be in a bound pose. File with extensions [pdb]" example: {'scFv': 'scfv.pdb', 'VHH': 'nb.pdb'} format: binary binderChain: type: string description: "Binder chain to design CDRs for" example: "A" cdrLengths: type: string description: "Provide a comma seperated list of CDR region lengths of the nanobody/scFv (ex. 11,8,18 means HCDR1 is 11 residues, HCDR2 is 8 residues, and HCDR3 is 18 residues). scFvs require 6 lengths to be defined (for heavy, then light chains)" example: {'scFv': '8,8,13,6,6,9', 'VHH': '11,8,18'} fwLengths: type: string description: "Provide a comma seperated list of framework region lengths of the nanobody/scFv (ex. 25,17,38,14 means HFW1 is 25 residues, HFW2 is 17 residues, HFW3 is 38 residues, and HFW4 is 14 residues). For scFvs, specify HFW1, HFW2, HFW3, HFW4+linker+LFR1, LFR2, LFR3, LFR4." example: {'scFv': '25,17,38,52,17,33,10', 'VHH': '25,17,38,14'} vhFirst: type: boolean description: "Specify whether the heavy chain is first in the sequence. [Only available when task is one of scFv]" example: True default: True vhLen: type: number description: "Length of the variable heavy domain. For scFvs, include the linker in the VH Length. [Only available when task is one of scFv]" example: {'scFv': 120} vlLen: type: number description: "Length of the variable light domain. [Only available when task is one of scFv]" example: {'scFv': 108} rosetta: type: boolean description: "Get in touch at info@tamarind.bio if you have a license and would like to use Germinal with Rosetta" default: False numDesigns: type: integer description: "Number of designs to generate. Germinal will generate designs until one is accepted or the job times out." default: 1 omitAAs: type: string description: "Comma seperated list of amino acids to omit from the design" default: "C" # Gnina Settings GninaSettings: type: object required: - proteinFile - ligandFile - boxX - boxY - boxZ - width - height - depth properties: proteinFile: type: string example: "1iep.pdb" format: binary ligandFile: type: string description: "sdf structure file for your receptor File with extensions [sdf]" example: "Conformer3D_COMPOUND_CID_5291.sdf" format: binary boxX: type: number description: "X coordinate of bounding box center" example: "15.190" default: 35 boxY: type: number description: "Y coordinate of bounding box center" example: "53.903" default: 27 boxZ: type: number description: "Z coordinate of bounding box center" example: "16.917" default: 35 width: type: number description: "Width of bounding box" example: "20" default: 20 height: type: number description: "Height of bounding box" example: "20" default: 20 depth: type: number description: "Depth of bounding box" example: "20" default: 20 cnnScoring: type: string description: "Amount of CNN scoring to use (metrorescore = metropolis+rescore, metrorefine = metropolis + refine" default: "rescore" enum: - "none" - "rescore" - "refinement" - "metrorefine" wholeProtein: type: boolean description: "Select to search the whole receptor for a binding pose. If true, box coordinates and size will be ignored" default: False exhaustiveness: type: number description: "Adjusts the amount of computational effort used during a docking experiment - increasing this to 32 will give a more consistent docking result" default: 8 scoreOnly: type: boolean description: "Score the provided ligand pose without docking. Returns CNN affinity and pose score for the input conformation as-is." default: False # Gromacs Settings GromacsSettings: type: object required: - systemType - uploadType - pdbFile - pdbID - proteinFile - ligandFile - forceField properties: systemType: type: string description: "Type of system to be simulated" default: "protein" enum: - "protein" - "protein-ligand" uploadType: type: string description: "Whether to upload a pdb file or fetch from PDB File with extensions [pdb]" default: "upload" enum: - "upload" - "fetch" pdbFile: type: string format: binary pdbID: type: string description: "PDB ID to fetch structure from PDB File with extensions [pdb]" proteinFile: type: string format: binary ligandFile: type: string format: binary forceField: type: string description: "Force field to use for simulation" default: "amber99sb" enum: - "amber99sb" - "amber99sb-ildn" - "amber14sb" boxType: type: string default: "cubic" enum: - "cubic" - "dodecahedron" - "triclinic" - "octahedron" waterModel: type: string default: "tip3p" enum: - "tip3p" - "tip4p" - "spc" salt: type: number minimum: 0 maximum: 1 default: 0.15 temp: type: number default: 300 saveFreq: type: number description: "Time interval (ps) at which frame is taken from the trajectory" minimum: 1 default: 10 NVTEquilibrationTime: type: number minimum: 0 default: 0.05 NPTEquilibrationTime: type: number description: "Number of nanoseconds (ns) to run NPT equilibration" minimum: 0 default: 0.05 simulationTime: type: number description: "Number of nanoseconds (ns) to run production simulation" minimum: 0 default: 1 trajFormat: type: string default: "xtc" enum: - "xtc" - "pdb" numReplicas: type: integer description: "Number of replicas (independent simulations) to run in parallel" maximum: 5 default: 1 # Gromacs-Custom Settings GromacsCustomSettings: type: object required: - inputFiles - init - restPrefix - miniPrefix - equiPrefix - prodPrefix - prodStep properties: inputFiles: type: array items: type: string description: "Input files for MD simulation File with extensions [mdp, gro, top, ndx]" format: binary init: type: string restPrefix: type: string miniPrefix: type: string equiPrefix: type: string prodPrefix: type: string prodStep: type: string awsInstanceType: type: string example: "g4dn.xlarge" numInstances: type: string example: "2" # Hbond-Strength Settings HbondStrengthSettings: type: object required: - inputType - smiles - sdfFile - xyzFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" - "xyz" smiles: type: string description: "SMILES string of the molecule [Only available when inputType is one of smiles]" example: "CC(=O)N" sdfFile: type: string description: "SDF/MOL file with 3D coordinates File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary xyzFile: type: string description: "XYZ coordinate file (e.g. from geometry optimization) File with extensions [xyz] [Only available when inputType is one of xyz]" format: binary charge: type: number description: "Net molecular charge" default: 0 multiplicity: type: number description: "Spin multiplicity (2S+1)" default: 1 numConformers: type: number description: "Number of conformers to generate and screen before computing ESP. More conformers = better sampling but slower" default: 20 # Highfold Settings HighfoldSettings: type: object required: - sequence properties: sequence: type: string description: "Include ':' to specify chain breaks for complex structure predictions" example: "SAKIDNLD" numModels: type: string description: "Number of models to be used, each generating a different prediction" default: "5" enum: - "1" - "2" - "3" - "4" - "5" numRecycles: type: number default: 3 numRelax: type: number default: 0 flag_nc: type: number default: 1 # Hmmalign Settings HmmalignSettings: type: object required: - inputType - fastaFile - csvFile - sequenceColumn properties: inputType: type: string default: "fasta" enum: - "fasta" - "csv" fastaFile: type: string format: binary csvFile: type: string format: binary sequenceColumn: type: string # Humatch Settings HumatchSettings: type: object required: - heavySequence - lightSequence properties: heavySequence: type: string description: "Heavy sequence of your antibody" example: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" lightSequence: type: string description: "Light sequence of your antibody" example: "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIN" # Hypermpnn Settings HypermpnnSettings: type: object required: - pdbFile - designedResidues properties: pdbFile: type: string description: "Protein structure file to be designed File with extensions [pdb]" example: "3HTN.pdb" format: binary designedChains: type: array items: type: string description: "Chain IDs to be designed (rest will be fixed)" example: ["A"] designedResidues: type: object description: "Residues to design in your protein" example: {'A': '60 61 62 63 64 65 66'} numSequences: type: number description: "Number of sequences to be generated for each protein backbone" default: 2 temperature: type: number description: "Model temperture - Suggested values 0.1, 0.15, 0.2, 0.25, 0.3. Higher values will lead to more diversity" minimum: 0 maximum: 1 default: 0.1 noiseLevel: type: string description: "Select from models of various noise levels (A)" default: "0.2" enum: - "0.02" - "0.1" - "0.2" - "0.3" omitAAs: type: string description: "These amino acids will be avoided when generating sequences" default: "C" verifySequences: type: string description: "Automatically perform structure prediction on generated sequences for verification" enum: - "verify-alphafold" - "verify-chai" # Idr Settings IdrSettings: type: object required: - sequenceFragment - templateFile properties: sequenceFragment: type: string example: "FNCREWCWN" maxLength: 40 templateFile: type: string description: "Template file to use for IDR analysis (ex. from walle library - https://github.com/drhicks/Kejia_peptide_binders/tree/7f65c18cc57b3e72d290c885c540276c7d9c6ab8/templates/walle) File with extensions [pdb]" example: "conf_2.pdb" format: binary # Igblast Settings IgblastSettings: type: object required: - inputType - organism - sequence - vGeneDatabase - dGeneDatabase - jGeneDatabase properties: inputType: type: string description: "" example: "Nucleotide" default: "Nucleotide" enum: - "Nucleotide" - "Amino Acid" organism: type: string description: "" default: "Human" enum: - "Human" - "Mouse" - "Rat" - "Rabbit" - "Rhesus Monkey" sequence: type: string description: " [Only available when inputType is one of Nucleotide, Amino Acid]" example: "GGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCCCCTTCAGTAACTACACCATGCACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTACTAGTAGTAGTAGTTACAGATATTACGCAGACTCAGTGGAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTTCTGTGTGAGAGATCGGGGCTATGATAGTAGTGGTTATTACGGAAATCTTGACTGCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCA" vGeneDatabase: type: string description: "IMGT V genes for the selected organism" default: "IMGT V genes (F+ORF+in-frame P)" enum: - "IMGT V genes (F+ORF+in-frame P)" dGeneDatabase: type: string description: "IMGT D genes for the selected organism [Only available when inputType is one of Nucleotide]" default: "IMGT D genes (F+ORF)" enum: - "IMGT D genes (F+ORF)" jGeneDatabase: type: string description: "IMGT J genes for the selected organism [Only available when inputType is one of Nucleotide]" default: "IMGT J genes (F+ORF+in-frame P)" enum: - "IMGT J genes (F+ORF+in-frame P)" vMismatchPenalty: type: number description: " [Only available when inputType is one of Nucleotide]" default: -1 minDMatches: type: number description: " [Only available when inputType is one of Nucleotide]" default: 5 dMismatchPenalty: type: number description: " [Only available when inputType is one of Nucleotide]" default: 2 alignmentExtension5: type: boolean description: " [Only available when inputType is one of Nucleotide]" default: False alignmentExtension3: type: boolean description: " [Only available when inputType is one of Nucleotide]" default: False # Igdesign Settings IgdesignSettings: type: object required: - task - pdbFile - heavyChain - lightChain - antigenChain - regions - condition_on_light_chain - condition_on_antigen - hcdr1Residues - hcdr2Residues - hcdr3Residues - lcdr1Residues - lcdr2Residues - lcdr3Residues properties: task: type: string description: "Antibody or nanobody input" example: "nanobody" default: "antibody" enum: - "antibody" - "nanobody" pdbFile: type: string description: "Antibody pdb to design sequences for File with extensions [pdb]" example: "9f6o.pdb" format: binary heavyChain: type: string description: "ID in pdb file of heavy chain" example: "B" lightChain: type: string description: "ID in pdb file of light chain [Only available when task is one of antibody]" example: "L" antigenChain: type: string description: "ID in pdb file of the antigen chain" example: "A" regions: type: string description: "Regions to mutate" example: ["hcdr3"] default: {'antibody': ['hcdr1', 'hcdr2', 'hcdr3', 'lcdr1', 'lcdr2', 'lcdr3'], 'nanobody': ['hcdr1', 'hcdr2', 'hcdr3']} enum: - "hcdr1" - "hcdr2" - "hcdr3" - "lcdr1" - "lcdr2" - "lcdr3" condition_on_light_chain: type: boolean description: "Condition design on light chain" default: False condition_on_antigen: type: boolean description: "Condition design on antigen" default: True numBatches: type: integer description: "Number of batches to design, each with 1000 designs" default: 1 selectCDRIndices: type: boolean description: "Select which residues are in CDRs instead of automatically detecting CDRs. IMGT numbered CDRs will be used by default. " default: False hcdr1Residues: type: string description: "Residues to keep fixed in the original pdb (starting from 1)" default: "" hcdr2Residues: type: string description: "Residues to keep fixed in the original pdb (starting from 1)" default: "" hcdr3Residues: type: string description: "Residues to keep fixed in the original pdb (starting from 1)" default: "" lcdr1Residues: type: string description: "Residues to keep fixed in the original pdb (starting from 1) [Only available when task is one of antibody]" default: "" lcdr2Residues: type: string description: "Residues to keep fixed in the original pdb (starting from 1) [Only available when task is one of antibody]" default: "" lcdr3Residues: type: string description: "Residues to keep fixed in the original pdb (starting from 1) [Only available when task is one of antibody]" default: "" # Iggm Settings IggmSettings: type: object required: - type - antigenFile - antigenChain - heavySequence - lightSequence properties: type: type: string description: "Antibody or nanobody" default: "antibody" enum: - "antibody" - "nanobody" antigenFile: type: string description: "Antigen structure File with extensions [pdb]" example: "8hpu_M_N_A.pdb" format: binary antigenChain: type: string description: "Antigen chain" example: "A" epitopeResidues: type: string description: "Epitope residues" heavySequence: type: string description: "Heavy chain sequence - use X for CDR regions" example: "VQLVESGGGLVQPGGSLRLSCAASXXXXXXXYMNWVRQAPGKGLEWVSVVXXXXXTFYTDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARXXXXXXXXXXXXXXWGQGTMVTVSS" lightSequence: type: string description: "Light chain sequence - use X for CDR regions" example: "DIQMTQSPSSLSASVGDRVSITCXXXXXXXXXXXWYQQKPGKAPKLLISXXXXXXXGVPSRFSGSGSGTDFTLTITSLQPEDFATYYCXXXXXXXXXXXFGGGTKVEIK" numDesigns: type: integer description: "Number of designs to generate" default: 1 # Immunebuilder Settings ImmunebuilderSettings: type: object required: - modelType - sequence1 - sequence2 properties: modelType: type: string default: "Antibody" enum: - "Antibody" - "Nanobody" - "TCR" sequence1: type: string description: "Protein sequence of heavy chain (for Antibody or Nanobody task) or alpha chain (for TCR task) to predict structure [Only available when modelType is one of Antibody, Nanobody, TCR]" example: "EVQLVESGGGVVQPGGSLRLSCAASGFTFNSYGMHWVRQAPGKGLEWVAFIRYDGGNKYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCANLKDSRYSGSYYDYWGQGTLVTVS" sequence2: type: string description: "Protein sequence of light chain (for Antibody task) or beta chain (for TCR task) to predict structure [Only available when modelType is one of Antibody, TCR]" example: "VIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDFK" # Intercaat Settings IntercaatSettings: type: object required: - pdbFile - queryChain - interactingChain properties: pdbFile: type: string description: "PDB file containing protein complex to analyze interfaces File with extensions [pdb]" example: "1cph.pdb" format: binary queryChain: type: string description: "Chain identifier for the query chain. Can also specify specific residues (e.g., 'A,6,7,8,9')" example: "B" interactingChain: type: string description: "Chain identifier(s) for the interacting chain(s). Use single letter or comma-separated list" example: "A" displayCompatibility: type: boolean description: "Show compatibility matrix of interface residues and their interactions" default: True displayContacts: type: boolean description: "Show detailed atomic interaction information" default: True searchRadius: type: number description: "Search radius for identifying atomic contacts (default 1.7Å if not specified)" minimum: 1 maximum: 5 default: 1.7 # Intfold Settings IntfoldSettings: type: object required: - inputFormat - sequence - molecules properties: inputFormat: type: string default: "sequence" enum: - "sequence" - "list" - "molecules" sequence: type: string description: "Protein sequence (use : to specify chainbreaks for multimers) [Only available when inputFormat is one of sequence]" example: "TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK:MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM" maxLength: 2048 molecules: type: string example: ["{'type': 'protein', 'sequence': 'TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQIL', 'chain': 'A'}"] proteins: type: string description: "List of protein sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK", "MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM"] rnas: type: string description: "List of RNA sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["GAGAGAGAAGTCAACCAGAGAAACACACCAACCCATTGCACTCCGGG", "TTGGTGGTATATTACCTGGTACGGGGGAAACTTCGTGGTGGCCGGCCACCTGACA"] dnas: type: string description: "List of DNA sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["GAGAGAGAAGTCAACCAGAGAAACACACCAACCCATTGCACTCCGGG", "TTGGTGGTATATTACCTGGTACGGGGGAAACTTCGTGGTGGCCGGCCACCTGACA"] addLigands: type: boolean description: "Add small molecule ligands to your structure prediction" default: False ligands: type: string description: "Specify your ligands (CCD code or smiles), use : to separate multiple ligands in one structure prediction (ex. CC:CC). Each new line is a separate set of ligands, to be paired with each protein sequence. [Only available when inputFormat is one of list, sequence]" example: ["SAH", "N[C@@H](Cc1ccc(O)cc1)C(=O)O"] modifications: type: object description: "Post-translational modifications to apply to the protein" default: [] model: type: string description: "IntelliFold model version" default: "v2" enum: - "v2" - "v1" - "v2-flash" numSamples: type: number description: "Number of samples" maximum: 100 default: 5 numBatches: type: integer description: "Will submit multiple parallel batches with numSamples designs each" maximum: 1000 default: 1 seed: type: number description: "Random seed to use with inference" numRecycles: type: number default: 10 outputType: type: string description: "Format of output structures" default: "pdb" enum: - "pdb" - "mmcif" # Ipc Settings IpcSettings: type: object required: - sequence properties: sequence: type: string # Ipsae Settings IpsaeSettings: type: object required: - inputType - pdbFile - cifFile - jsonFile - npzFile - plddtFile - confidenceFile - pae_cutoff - dist_cutoff properties: inputType: type: string default: "af2" enum: - "af2" - "boltz" pdbFile: type: string format: binary cifFile: type: string format: binary jsonFile: type: string format: binary npzFile: type: string format: binary plddtFile: type: string format: binary confidenceFile: type: string format: binary pae_cutoff: type: number description: "Cutoff for PAE" default: 10 dist_cutoff: type: number description: "Cutoff for distance" default: 10 # Its-Flexible Settings ItsFlexibleSettings: type: object required: - pdbFile - ab_chains - chain - resi_start - resi_end - predictor properties: pdbFile: type: string description: "Antibody/TCR structure file in PDB format File with extensions [pdb]" example: "8jbj.pdb" format: binary ab_chains: type: array items: type: string description: "Labels of all chains included in context (e.g., heavy & light chain)" example: "A,B" chain: type: string description: "Chain containing the loop to predict" example: "A" resi_start: type: string description: "First residue included in loop (IMGT 107 for loop predictor, 105 for anchors predictor)" example: "107" resi_end: type: string description: "Last residue included in loop (IMGT 116 for loop predictor, 118 for anchors predictor)" example: "116" predictor: type: string description: "Predictor type: loop (alignment on loop residues) or anchors (alignment on Fv residues)" default: "loop" enum: - "loop" - "anchors" # Legolas Settings LegolasSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure in pdb format File with extensions [pdb]" example: "1a3n.pdb" format: binary # Libinvent Settings LibinventSettings: type: object required: - scaffold properties: scaffold: type: string description: "replace your locations to decorate with [*:1], [*:2], etc" example: "[*:1]Cc2cnc1cncc(C[*:2])c1c2" numDesigns: type: number description: "Number of designs to generate" minimum: 5 default: 100 sample_strategy: type: string description: "Sampling strategy: 'beamsearch' (deterministic, default) or 'multinomial'" default: "beamsearch" enum: - "beamsearch" - "multinomial" temperature: type: number description: "Temperature for multinomial sampling (only used when sample_strategy is 'multinomial')" default: 1 # Lichen Settings LichenSettings: type: object required: - heavyChain properties: task: type: string description: "Generate: Create light chains for each heavy chain. Bispecific: Generate common light chains for pairs of heavy chains (requires even number of sequences)." default: "generate" enum: - "generate" - "bispecific" heavyChain: type: string description: "Single sequence, or FASTA formatted text. For bispecific: provide pairs of sequences (must be even number)." example: "EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDGKYYYGMDVWGQGTTVTVSS" numSequences: type: number description: "Number of light chain sequences to generate. For generate task: per heavy chain. For bispecific task: per heavy chain pair." default: "10" germlineSeed: type: string description: "V-gene type, family, or specific genes (e.g., 'IGKV1', 'IGLV1', or 'IGKV1 IGKV2'). Leave empty for unrestricted generation." customSeed: type: string description: "Custom amino acid seed sequence for the light chain (e.g., 'DIQMTQ')" cdrL1: type: string description: "Specify CDR-L1 sequence for grafting (IMGT or Kabat definition)" cdrL2: type: string description: "Specify CDR-L2 sequence for grafting (IMGT or Kabat definition)" cdrL3: type: string description: "Specify CDR-L3 sequence for grafting (IMGT or Kabat definition)" numberingScheme: type: string description: "Numbering scheme for CDR definition when using CDR grafting" default: "IMGT" enum: - "IMGT" - "Kabat" filtering: type: string description: "Space-separated filtering steps: 'redundancy', 'diversity', 'ANARCI', 'Humatch', 'AbLang2'. Example: 'redundancy diversity Humatch'" # Ligandmpnn Settings LigandmpnnSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure file to be designed File with extensions [pdb]" example: "3HTN.pdb" format: binary designedChains: type: array items: type: string description: "Chain IDs to be designed (rest will be fixed)" example: ["A"] designedResidues: type: object description: "Residues to design in your protein, can be ranges or individual residues" example: {'A': '60 61 62 63 64 65 66'} default: {} numSequences: type: number description: "Number of sequences to be generated for each protein backbone" default: 2 temperature: type: number description: "Model temperture - Suggested values 0.1, 0.15, 0.2, 0.25, 0.3. Higher values will lead to more diversity" minimum: 0 maximum: 1 default: 0.1 noiseLevel: type: string description: "Select from models of various noise levels (A)" default: "0.2" enum: - "0.02" - "0.1" - "0.2" - "0.3" omitAAs: type: string description: "These amino acids will be avoided when generating sequences" default: "C" bias_AA: type: string description: "Bias toward/against specific amino acids, as comma separated list. Example: W:3.0,P:3.0,C:3.0,A:-3.0" example: "W:3.0,P:3.0,C:3.0,A:-3.0" bias_AA_per_residue: type: string description: "Bias amino acids per residue, as dictionary. Example: {\"C1\": {\"G\": -0.3, \"C\": -2.0, \"P\": 10.8}, \"C3\": {\"P\": 10.0}, \"C5\": {\"G\": -1.3, \"P\": 10.0}, \"C7\": {\"G\": -1.3, \"P\": 10.0}}" example: "{\"C1\": {\"G\": -0.3, \"C\": -2.0, \"P\": 10.8}, \"C3\": {\"P\": 10.0}, \"C5\": {\"G\": -1.3, \"P\": 10.0}, \"C7\": {\"G\": -1.3, \"P\": 10.0}}" omit_AA_per_residue: type: string description: "Specify amino acids to exclude at specific residue positions. To force a specific amino acid, omit all others. Example: {\"A1\": \"CP\", \"A2\": \"CW\"} will prevent C,P at position A1 and C,W at position A2." example: "{\"A1\": \"CP\", \"A2\": \"CW\"}" homo_oligomer: type: number description: "Number of copies of the protein (ex. 2 for dimer, 3 for trimer, etc.)" # Logp Settings LogpSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string description: "SMILES string of the molecule [Only available when inputType is one of smiles]" example: "c1ccccc1" sdfFile: type: string description: "SDF/MOL file File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary method: type: string description: "crippen: fast atom-contribution model (instant). xtb: physics-based via solvation free energies (~30s)" default: "crippen" enum: - "crippen" - "xtb" charge: type: number description: "Net molecular charge (for xTB method only)" default: 0 # Mage Settings MageSettings: type: object required: - rbdPrompt properties: rbdPrompt: type: string description: "Amino acid sequence of the antigen target (signal peptides and transmembrane regions should be removed)" example: "RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF" numSequences: type: number description: "Number of antibody sequences to generate" default: "10" # Masif Settings MasifSettings: type: object required: - pdbFile - chain properties: pdbFile: type: string format: binary chain: type: string example: "A" # Mavenets-Finetune Settings MavenetsFinetuneSettings: type: object required: - baseModel - trainFile - validFile - epochs - learningRate - batchSize - seed - hiddenLayers - numBlocks - numHeads - embeddingSize - mhaDropout - mlpDropout - finalDropout - finalLayers properties: baseModel: type: string description: "Base model to use for finetuning" default: "mlp" enum: - "mlp" - "transformer" trainFile: type: string description: "CSV file containing your ids, sequences, and fitness value File with extensions [csv]" format: binary validFile: type: string description: "CSV file containing your ids, sequences, and fitness value File with extensions [csv]" format: binary epochs: type: number description: "Number of Epochs to train the model for" default: 1000 learningRate: type: number description: "Learning rate for model training (default: 3e-4)" default: 0.0003 batchSize: type: number description: "Training batch size per GPU" default: 32 seed: type: number description: "Random seed for reproducibility" default: 42 hiddenLayers: type: string description: "Comma-separated list of hidden layer sizes (e.g. '128,32' or '256,128,64') [Only available when baseModel is one of mlp]" default: "128,32" numBlocks: type: number description: "Number of transformer blocks (n_transformers) [Only available when baseModel is one of transformer]" default: 4 numHeads: type: number description: "Number of attention heads per block [Only available when baseModel is one of transformer]" default: 8 embeddingSize: type: number description: "Size of the embedding vector [Only available when baseModel is one of transformer]" default: 32 mhaDropout: type: number description: "Dropout rate for Multi-Head Attention [Only available when baseModel is one of transformer]" default: 0.2 mlpDropout: type: number description: "Dropout rate for the MLP inside transformer blocks [Only available when baseModel is one of transformer]" default: 0.1 finalDropout: type: number description: "Dropout rate for the final classification head [Only available when baseModel is one of transformer]" default: 0.2 finalLayers: type: number description: "Number of layers in the final classification head [Only available when baseModel is one of transformer]" default: 1 # Mavenets-Inference Settings MavenetsInferenceSettings: type: object required: - inferenceMode - inputCsv - sequenceColumn - startSequence - mcmcSteps - beta - nativeBias - maxMutations properties: inferenceMode: type: string description: "Choose between scoring a CSV of sequences or running MCMC evolution" default: "score" enum: - "score" - "mcmc" inputCsv: type: string description: "Upload CSV containing protein sequences File with extensions [csv] [Only available when inferenceMode is one of score]" format: binary sequenceColumn: type: string description: "Select the column containing the protein sequences [Only available when inferenceMode is one of score]" startSequence: type: string description: "The amino acid sequence to start the simulation from (e.g., Wild Type) [Only available when inferenceMode is one of mcmc]" mcmcSteps: type: number description: "Number of steps to run the Metropolis-Hastings simulation [Only available when inferenceMode is one of mcmc]" default: 100000 beta: type: number description: "Controls selection pressure. Negative values favor high fitness. (e.g. -10 to -35) [Only available when inferenceMode is one of mcmc]" default: -10 nativeBias: type: number description: "Bias towards the starting sequence (0.0 to 1.0) to prevent drifting too far [Only available when inferenceMode is one of mcmc]" default: 0.9 maxMutations: type: number description: "Maximum number of mutations allowed from the starting sequence [Only available when inferenceMode is one of mcmc]" default: 9 # Mber Settings MberSettings: type: object required: - task - pdbFile - targetChains properties: task: type: string description: "Type of design task to perform" default: "Binder Design" enum: - "Binder Design" pdbFile: type: string description: "Target protein structure for binder design (PDB format) File with extensions [pdb]" example: "9f6o.pdb" format: binary targetChains: type: array items: type: string description: "Chain IDs of target (comma-separated for multiple chains, e.g., A,B) [Only available when task is one of Binder Design]" example: "A" default: "A" hotspotResidues: type: string description: "Specify epitope residues on your target protein for the VHH binder to focus on during design. Enter residue numbers separated by commas (e.g., 305,456). If left empty, mBER will automatically detect suitable hotspots." example: "305,456" default: "" vhhSequence: type: string description: "VHH template sequence with asterisks (*) marking positions to be designed" example: "QVQLVESGGGLVQPGGSLRLSCAASGFTF***AMSWVRQAPGKGLEWVS**************YADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAA**************WGQGTQVTVSS" numDesigns: type: integer description: "Number of binder designs to generate" default: 1 temperature: type: number description: "Temperature parameter for sequence sampling" minimum: 0.1 maximum: 2 default: 1 steps: type: number description: "Number of optimization steps for trajectory design" minimum: 10 maximum: 1000 default: 100 seed: type: number description: "Random seed for reproducible results" example: 42 relax: type: string description: "Perform amber relaxation for more accurate side chain predictions (currently disabled)" default: False enum: - "False" plmModel: type: string description: "Model used for sequence guidance during binder design." default: "ESM" enum: - "ESM" - "Ablang2" # Md-Openmm Settings MdOpenmmSettings: type: object required: - task - pdbFile - complexFile - ligandCode - sdfFile - minimizationSteps - equilibrationTime - productionTime properties: task: type: string description: "Task to perform" default: "protein" enum: - "protein" - "protein-ligand" - "protein-ligand-complex" pdbFile: type: string description: "PDB structure file for your protein File with extensions [pdb] [Only available when task is one of protein, protein-ligand]" format: binary complexFile: type: string description: "PDB structure file for your protein File with extensions [pdb] [Only available when task is one of protein-ligand-complex]" format: binary ligandCode: type: string description: "Code for your ligand [Only available when task is one of protein-ligand-complex]" sdfFile: type: string description: "SDF structure file for your ligand File with extensions [sdf] [Only available when task is one of protein-ligand]" format: binary minimizationSteps: type: string description: "Number of minimization steps" default: "1000" enum: - "1000" - "5000" - "10000" - "20000" - "50000" - "100000" equilibrationTime: type: number description: "" default: 0.2 productionTime: type: number description: "" default: 2 integrationTimestep: type: string description: "Integration timestep (fs)" default: "2" enum: - "0.5" - "1" - "2" - "3" - "4" equilibrationTemperature: type: string description: "Equilibration temperature (K)" default: "298" equilibrationPressure: type: string description: "Equilibration pressure (atm)" default: "1" # Mdgen Settings MdgenSettings: type: object required: - task - pdbFile - xtcFile properties: task: type: string default: "Forward Simulation" enum: - "Forward Simulation" pdbFile: type: string format: binary xtcFile: type: string format: binary numFrames: type: number description: "Number of frames that MDGen generates" default: 1000 # Membrane-Gromacs Settings MembraneGromacsSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Upload a PDB file of the membrane protein. Cofactors, ligands, ions, and crystal waters will be automatically removed during cleanup. Missing residues and atoms will be rebuilt. File with extensions [pdb]" example: "2IC8.pdb" format: binary membranePreset: type: string description: "Select a biological membrane preset or choose Custom to specify lipid composition manually." default: "custom" enum: - "custom" - "plasma" - "ecoli-inner" - "ecoli-outer" - "er" - "mitochondrial-inner" - "mitochondrial-outer" lipidUpperLeaflet: type: string description: "Lipid composition as NAME:RATIO pairs. Examples: 'POPC' (pure), 'POPC:7 CHOL:3' (70% POPC + 30% cholesterol), 'POPC:4 POPE:3 POPS:2 CHOL:1' (complex mixture). Supported with Martini 3 (8): CHOL, DLPE, DOPC, DPPC, POPC, POPE, POPG, POPI. Additional with Martini 2 fallback (12): DGPC, DLPC, DNPC, DOPE, DOPG, DOPS, DPG1, DPG3, DPPE, ERGO, POP2, POPS." default: "POPC" lipidLowerLeaflet: type: string description: "Lower leaflet composition. Use 'same' for symmetric bilayer, or specify composition like upper leaflet." default: "same" membraneType: type: string description: "Membrane type for PPM3 protein orientation. Auto-set when using a membrane preset." default: "PMm" enum: - "PMm" - "PMp" - "PMf" - "ERm" - "ERf" - "MOM" - "MIM" - "GnO" - "GnI" - "GpI" - "THp" - "ARC" cgEquilibrationTime: type: number description: "Coarse-grained equilibration time for lipid packing. 500 ns typically sufficient." minimum: 1 maximum: 5000 default: 500 salt: type: number minimum: 0 maximum: 1 default: 0.15 temp: type: number description: "Simulation temperature. 310 K is physiological." minimum: 280 maximum: 350 default: 310 simulationTime: type: number minimum: 0.01 maximum: 1000 default: 10 saveFreq: type: number minimum: 1 maximum: 100 default: 10 numReplicas: type: integer minimum: 1 maximum: 3 default: 1 # Mhc-Fine Settings MhcFineSettings: type: object required: - sequence properties: sequence: type: string description: "Sequence of MHC-peptide complex, separated by :" example: "GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRT:HMTEVVRHC" # Microscopic-Pka Settings MicroscopicPkaSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string description: "SMILES string of the molecule [Only available when inputType is one of smiles]" example: "CC(=O)O" sdfFile: type: string description: "SDF/MOL file File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary method: type: string description: "Energy method for pKa prediction" default: "xtb-gfn2" enum: - "xtb-gfn2" charge: type: number description: "Net molecular charge of the starting (protonated) state" default: 0 solvent: type: string description: "pKa is computed in aqueous solution" default: "water" enum: - "water" # Min-Distance-Selected-Residues Settings MinDistanceSelectedResiduesSettings: type: object required: - pdbFile - chains1 - residues1 - chains2 - residues2 properties: pdbFile: type: string format: binary chains1: type: array items: type: string description: "Chains to compute RMSD on" allResiduesChain1: type: boolean description: "Whether to compute RMSD on all residues in chain 1" default: False residues1: type: object description: "Residues to compute RMSD on" chains2: type: array items: type: string description: "Chains to compute RMSD on" allResiduesChain2: type: boolean description: "Whether to compute RMSD on all residues in chain 2" default: False residues2: type: object description: "Residues to compute RMSD on" # Modelangelo Settings ModelangeloSettings: type: object required: - map properties: map: type: string description: "CryoEM density map to use in structure prediction File with extensions [mrc]" format: binary sequence: type: string description: "Protein sequence (use : to separate chains)" # Molecular-Descriptors Settings MolecularDescriptorsSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string description: "SMILES string of the molecule [Only available when inputType is one of smiles]" example: "CC(=O)Oc1ccccc1C(=O)O" sdfFile: type: string description: "SDF/MOL file File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary descriptorSet: type: string description: "Which descriptors to compute. 'all' gives 200+ descriptors including MW, LogP, TPSA, QED, Lipinski rules, and fingerprints" default: "all" enum: - "all" - "physicochemical" - "druglikeness" - "fingerprints" # Molprobity Settings MolprobitySettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure in pdb format File with extensions [pdb]" example: "1a3n.pdb" format: binary # Mosaic-Hallucinate Settings MosaicHallucinateSettings: type: object required: - targetSequence - binderLength - numDesigns properties: targetSequence: type: string description: "Target Protein amino acid sequence to design binder to, use : to separate chains for multimers" example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" maxLength: 5000 binderLength: type: number description: "Length of the binder to design (fixed length optimization)" default: 220 numDesigns: type: number description: "Number of designs (sequence and structure codesign) to generate" default: 1 # Mrnabert Settings MrnabertSettings: type: object required: - task - sequence - sequenceType - saveEmbeddingsFormat - optimizationSteps properties: task: type: string description: "Select the mRNABERT task to run" default: "score_sequence" enum: - "score_sequence" - "mutation_scan" - "codon_optimize" - "extract_embedding" sequence: type: string description: "mRNA sequence (A/C/G/U/T). For 'complete' mode, wrap the CDS region in [...]. CDS-only sequences must have length divisible by 3. Paste a FASTA or upload a CSV to run as a batch — each sequence becomes its own subjob." example: "GCCGCCACC[ATGGTGAGCAAGGGCGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTTAA]GCGACGCGACGGCGA" sequenceType: type: string description: "How to tokenize the sequence. Matches the preprocessing in the mRNABERT paper." default: "complete" enum: - "complete" - "codon" - "utr" saveEmbeddingsFormat: type: string description: "How to extract or aggregate the embeddings [Only available when task is one of extract_embedding]" default: "mean" enum: - "mean" - "raw" - "cls" optimizationSteps: type: number description: "Number of random-coordinate descent steps. Each step picks a CDS codon, tries all synonymous substitutions, and accepts the best if it raises the PLL. [Only available when task is one of codon_optimize]" default: 50 randomSeed: type: number description: "Seed controlling the order in which codon positions are visited. Leave blank for a fresh random seed each run. [Only available when task is one of codon_optimize]" # Msa Settings MsaSettings: type: object required: - sequence properties: sequence: type: string description: "Sequence to generate MSA for" example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" msaDatabase: type: string description: "Select how the MSA is generated using UniRef30, SwissProt, and the ColabFold environmental database." example: "uniref" default: "uniref" enum: - "uniref" - "swissprot" - "uniref+swissprot" monomer_msa: type: boolean description: "Whether to generate a separate MSA for each chain, or a single MSA for the entire complex" default: False # Msa-Analysis Settings MsaAnalysisSettings: type: object required: - fastaFile properties: fastaFile: type: string description: "FASTA file containing multiple protein sequences to align (2-10,000 sequences) File with extensions [fasta, fa]" example: ">seq1 MTKLLLLLLLLAAVAVA >seq2 MTKLLLLLLLLAAVAVT >seq3 MTKLLLLLLLLAAIAVA" format: binary algorithm: type: string description: "auto (recommended), clustal (high accuracy), muscle (balanced), mafft-fast (large datasets), mafft-accurate (divergent sequences)" default: "auto" enum: - "auto" - "clustal" - "muscle" - "mafft-fast" - "mafft-accurate" output_format: type: string description: "Alignment output format" default: "fasta" enum: - "fasta" - "clustal" - "phylip" - "stockholm" # Msa-Cluster Settings MsaClusterSettings: type: object required: - fastaFile properties: fastaFile: type: string description: "Sequences to cluster File with extensions [fasta, fa]" format: binary # Multi-Evolve Settings MultiEvolveSettings: type: object required: - task - wtFiles - trainingDatasetFile - mutationPoolFile - mode - topMutsPerLoad - mutationsFile - wtDnaFasta - overhang - species - oligoDirection - tm - output - oligosFile - wtSequence - pdbFiles - chainId - variants - normalizingMethod properties: task: type: string default: "train_propose" enum: - "train_propose" - "assembly_design" - "zeroshot_ensemble" wtFiles: type: string description: "Wildtype FASTA input. Single-chain: upload one FASTA. Multi-chain complexes: upload one FASTA per chain, in the same order used by mutation columns (chain1, chain2, ...). File with extensions [fasta, fa] [Only available when task is one of train_propose]" example: "apex.fasta" format: binary trainingDatasetFile: type: string description: "Training CSV with mutation and property_value columns (for multi-chain, use slash-separated mutations in chain order, e.g. A10V/B25M). MULTI-evolve ranks higher predicted values as better; if your assay metric is lower-is-better (e.g. IC50/Kd), transform labels before upload (e.g. -log10 or negate). File with extensions [csv] [Only available when task is one of train_propose]" example: "example_dataset.csv" format: binary mutationPoolFile: type: string description: "Single-column mutation pool (one mutation per row, no header) used for combinatorial proposal search. File with extensions [csv] [Only available when task is one of train_propose]" example: "combo_muts.csv" format: binary mode: type: string description: "test runs a quick pass; standard performs full training grid [Only available when task is one of train_propose]" default: "standard" enum: - "test" - "standard" topMutsPerLoad: type: number description: "Top variants kept for each mutation load (3 to 10 mutations), ranked by ensemble prediction score (higher is better). Total exported rows are up to 8 x this value. [Only available when task is one of train_propose]" minimum: 1 maximum: 500 default: 3 mutationsFile: type: string description: "CSV (no header) containing mutation strings to assemble File with extensions [csv] [Only available when task is one of assembly_design]" example: "MULTI-assembly_input.csv" format: binary wtDnaFasta: type: string description: "Wildtype DNA sequence FASTA with symmetric overhangs File with extensions [fasta, fa] [Only available when task is one of assembly_design]" example: "APEX_33overhang.fasta" format: binary overhang: type: number minimum: 0 default: 33 species: type: string description: "Codon usage table for oligo design [Only available when task is one of assembly_design]" default: "human" enum: - "human" - "ecoli" - "yeast" oligoDirection: type: string default: "bottom" enum: - "top" - "bottom" tm: type: number default: 80 output: type: string description: "design creates new cloning_sheet.csv + oligos.csv; update re-syncs cloning_sheet.csv IDs from uploaded oligos.csv. [Only available when task is one of assembly_design]" default: "design" enum: - "design" - "update" oligosFile: type: string description: "Required when Output Mode is update; upload oligos.csv from a prior design run File with extensions [csv] [Only available when task is one of assembly_design]" format: binary wtSequence: type: string description: "Provide wildtype sequence directly or upload a WT FASTA using the sequence input options [Only available when task is one of zeroshot_ensemble]" example: "MGKSYPTVSADYQDAVEKAKKKLRGFIAEKRCAPLMLRLAFHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPKVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFADA" pdbFiles: type: string description: "One or more PDB/CIF files used for ESM-IF scoring File with extensions [pdb, cif] [Only available when task is one of zeroshot_ensemble]" example: "apex.cif" format: binary chainId: type: string description: "Single chain used for ESM-IF scoring (applies to all uploaded structure files) [Only available when task is one of zeroshot_ensemble]" default: "A" variants: type: number minimum: 1 default: 24 normalizingMethod: type: string description: "aa_substitution_type groups by WT->mutant residue type (e.g. A->V); aa_mutation groups by mutant residue only (e.g. V). [Only available when task is one of zeroshot_ensemble]" default: "aa_substitution_type" enum: - "aa_substitution_type" - "aa_mutation" excludedPositions: type: string description: "Comma-separated 1-based residue positions to exclude from mutation (e.g. 1,14,41). [Only available when task is one of zeroshot_ensemble]" default: "" # N-Linked-Glycosylation Settings NLinkedGlycosylationSettings: type: object required: - sequence properties: sequence: type: string example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" # Nampnn Settings NampnnSettings: type: object required: - mode - pdbFile properties: mode: type: string description: "Mode to run the model in" default: "design" enum: - "design" - "specificity" pdbFile: type: string description: "Protein structure file to be designed File with extensions [pdb]" example: "9f6o.pdb" format: binary numSequences: type: number description: "Number of sequences to be generated for each protein backbone [Only available when mode is one of design]" default: 2 # Nbforge Settings NbforgeSettings: type: object required: - sequence properties: sequence: type: string description: "Nanobody (VHH) amino acid sequence" example: "QVKLEESGGGLVQPGGSLRLSCAGTGWTLEFYAIAWYRQAPGKERELVSCISSSSESNTYEDSVKGRFAMSRDKSRNTAWLQMNNLKPADSGVYYCAALPNMNCIREVMQYVDEWGQGTPVTVSS" noMinimize: type: boolean description: "Skip OpenMM energy minimization of the predicted structure" default: False # Netmhcpan Settings NetmhcpanSettings: type: object required: - inputType - sequence - peptide properties: inputType: type: string default: "sequence" enum: - "sequence" - "peptide" sequence: type: string example: "ASQKRPSQRHGSKYLATASTMDHARHGFLPRHRDTGILDSIGRFFGGDRGAPKNMYKDSHHPARTAHYGSLPQKSHGRTQDENPVVHFFKNIVTPRTPPPSQGKGRKSAHKGFKGVDAQGTLSKIFKLGGRDSRSGSPMARRELVISLIVES" peptide: type: string example: ["AAAGAEAGKATTE"] alleles: type: string description: "Comma-separated list of HLA alleles to test for peptide binding (e.g., DRB1_1664,H-2-IAd). Leave empty to use default alleles. For list of valid alleles see https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.3/" example: "DRB1_1664,H-2-IAd" # Netsolp Settings NetsolpSettings: type: object required: - sequence properties: sequence: type: string description: "Protein sequence to assess solubility" # Nos Settings NosSettings: type: object required: - csvFile - heavySequenceColumn - lightSequenceColumn - labelColumn - modelType properties: csvFile: type: string description: "CSV file containing your sequences and property of interest File with extensions [csv]" format: binary heavySequenceColumn: type: string description: "Title of heavy sequence column" lightSequenceColumn: type: string description: "Title of light sequence column" labelColumn: type: string description: "Column that contains a value for each sequence, which you want to optimize for (increase)" learningRate: type: number description: "Model learning rate (between 0 and 1)" default: 0.005 modelType: type: string description: "Type of model to train" default: "mlm" enum: - "mlm" noiseScale: type: number description: "Noise scale for Gaussian model (between 2 and 10)" default: 5 batchRatio: type: number description: "Ratio of Generative Loss Updates to Discriminative" default: 5 # Nos-Inference Settings NosInferenceSettings: type: object required: - heavyChain - lightChain - regions properties: heavyChain: type: string description: "Heavy chain sequence" example: "EVQLVESGGGLVQPGRSMKLSCAASGFTFNNYDMAWVCQAPKKGLEWVATISYDGSSTYYRDSVKGRFTISRDNIKSTLYLQMDSLRSEDTATYYCARQARGFAYWGQGTLVTVSS" lightChain: type: string description: "Light chain sequence" example: "DIQMTQSPASLSASLGETVTIECLASEDIYSNLAWYQQKPGKSPQLLIYDASSLQDGVPSRFSGSESGTQYSLEINSLQSEDAATYFCQQHHDYPLTFGSGTKLEIK" regions: type: string description: "The model will mutate the selected regions (aho numbering) while keeping other regions fixed" default: ['hcdr1', 'hcdr2'] enum: - "hcdr1" - "hcdr2" - "hcdr3" - "lcdr1" - "lcdr2" - "lcdr3" # Oas Settings OasSettings: type: object required: - sequence properties: sequence: type: string description: "Input sequence with which to query OAS" example: "EVQLVESGGGLVQAGGSLRLSCAASGRTFSNYHMAWFRQAPGKEREFVAGISWTGRGTYYTDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAEGTLYGSGGRTHQSAYDYWGQGTQVTVSS" maxLength: 10000 species: type: string description: "Species to search against in OAS" example: "Human" default: "Any" enum: - "Any" - "Human" - "Mouse" - "Rat" chain: type: string description: "Type of chain to search against in OAS" example: "Heavy" default: "Any" enum: - "Any" - "Heavy" - "Light" maxResults: type: number description: "Maximum number of sequences to report in OAS results (1-100)" example: 50 minimum: 1 maximum: 100 default: 50 regions: type: string description: "Regions of the antibody to search against in OAS" example: "whole" default: "whole" enum: - "whole" - "cdrs" - "cdr3" lengthMatch: type: boolean description: "Search only for sequences with a matched length" example: False default: False # Odesign-Antibody Settings OdesignAntibodySettings: type: object required: - task - antigen - antigenChains - antigenResidues - vhSequence - vhLengths - vlSequence - vlLengths properties: task: type: string description: "Type of antibody to design" default: "scfv" enum: - "scfv" - "nanobody" antigen: type: string description: "Antigen structure file (PDB or CIF format) File with extensions [pdb, cif]" example: "6oq5_tcdb_truncated.pdb" format: binary antigenChains: type: array items: type: string description: "Chain IDs from the antigen structure to use as target" example: ["A"] hotspot: type: object description: "Optional hotspot residues on the antigen for antibody targeting" example: {'A': '538, 151, 152, 148, 539'} antigenResidues: type: object description: "Residue range from antigen structure to include in design" example: {'A': '100-550'} vhSequence: type: string description: "Heavy chain framework sequence with hyphens (-) marking CDRs to design" example: {'scfv': 'EVQLVESGGGLVQPGGSLRLSCAAS-YIHWVRQAPGKGLEWVARI-TRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSR-WGQGTLVTVSS', 'nanobody': 'QVQLVESGGGLVQPGGSLRLSCAAS-FSLGWFRQAPGQGLEAVAAI-TYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAA-WGQGTLVTVS'} vhLengths: type: string description: "Target length range for each masked CDR in VH. Format: min-max for each CDR, comma-separated (e.g., 6-7,6-7,9-15)" example: "6-7,6-7,9-15" vlSequence: type: string description: "Light chain framework sequence with hyphens (-) marking CDRs to design. [Only available when task is one of scfv]" example: "DIQMTQSPSSLSASVGDRVTITC-WYQQKPGKAPKLLIY-GVPSRFSGSRSGTDFTLTISSLQPEDFATYYC-FGQGTKVEIK" vlLengths: type: string description: "Target length range for each masked CDR in VL. Format: min-max for each CDR, comma-separated (e.g., 6-7,6-7,9-15) [Only available when task is one of scfv]" example: "6-7,6-7,9-15" # Omegafold Settings OmegafoldSettings: type: object required: - sequence properties: sequence: type: string description: "Protein amino acid sequence" example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" # Openfe Settings OpenfeSettings: type: object required: - simulationType - proteinPDB - networkType - ligandsSDF - ligandFile - nvtLength - atomMapper - max3d - chargeMethod - protocolRepeats - equilLength - prodLength properties: simulationType: type: string description: "Choose the type of simulation to run" default: "complexMD" enum: - "rbfe" - "complexMD" proteinPDB: type: string description: "Protein structure in pdb format File with extensions [pdb]" format: binary networkType: type: string description: "How ligands are connected in the perturbation network" default: "minimal_spanning" enum: - "minimal_spanning" - "minimal_redundant" - "star_map" - "custom" ligandsSDF: type: string description: "Ligands in sdf format File with extensions [sdf]" format: binary alchemicalNetwork: type: string description: "Interactive preview and editor for the ligand perturbation network" networkEdges: type: string ligandFile: type: string description: "Ligand file in sdf format File with extensions [sdf]" format: binary nvtLength: type: number description: "Length of the NVT phase (ps)" minimum: 0 maximum: 1000 default: 100 atomMapper: type: string description: "Algorithm for mapping atoms between ligand pairs. Kartograf is newer and often produces better mappings for complex transformations." default: "lomap" enum: - "lomap" - "kartograf" max3d: type: number description: "Maximum 3D distance between mapped atoms in Angstroms. Lower values require better-aligned ligand poses. Increase if atom mapping fails on unaligned ligands." minimum: 0.1 maximum: 1000 default: 1 chargeMethod: type: string description: "Method for assigning partial charges to ligands. AM1-BCC is the standard method. NAGL uses a graph neural network and is faster." default: "am1bcc" enum: - "am1bcc" - "nagl" protocolRepeats: type: number description: "Number of independent repeats per transformation. Minimum 2 required for error estimation." minimum: 2 maximum: 5 default: 3 equilLength: type: number description: "Length of the equilibration phase (ps)" minimum: 0 maximum: 10000 default: 1000 prodLength: type: number description: "Length of the production phase (ps)" minimum: 0 maximum: 10000 default: 5000 # Openfold Settings OpenfoldSettings: type: object required: - inputFormat - sequence - molecules properties: inputFormat: type: string default: "sequence" enum: - "sequence" - "molecules" sequence: type: string description: "Protein sequence (use : to specify chainbreaks for multimers) [Only available when inputFormat is one of sequence]" example: "TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQIL" molecules: type: string example: ["{'type': 'protein', 'sequence': 'TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQIL', 'chain': 'A'}", "{'type': 'protein', 'sequence': 'MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM', 'chain': 'B'}", "{'inputType': 'ccd', 'chain': 'L', 'ccdCode': 'ATP', 'type': 'ligand'}"] addLigands: type: boolean description: "Add small molecule ligands to your structure prediction [Only available when inputFormat is one of sequence]" default: False ligands: type: string description: "Specify your ligands (CCD code or smiles), use : to separate multiple ligands in one structure prediction (ex. CC:CC). Each new line is a separate set of ligands, to be paired with each protein sequence. [Only available when inputFormat is one of sequence]" example: ["SAH", "N[C@@H](Cc1ccc(O)cc1)C(=O)O"] templateMode: type: string description: "Use no templates, automatic PDB100 templates, or uploaded custom template CIFs." default: "none" enum: - "none" - "pdb100" - "custom" templateFiles: type: string description: "Custom template mmCIF files for template-guided protein inference. File with extensions [cif]" format: binary templateMapping: type: string description: "Map each query chain to the corresponding chain in each uploaded template file." example: ["{'templateName': 'input.cif', 'mappings': [{'boltzChainID': 'A', 'templateChainID': 'B'}]}"] outputFormat: type: string default: "pdb" enum: - "pdb" - "cif" numSeeds: type: number description: "Number of diffusion samples to generate per prediction." default: 5 chooseBest: type: boolean description: "Return only the best confidence model (by ranking score) or all generated models" default: True # Openmm Settings OpenmmSettings: type: object required: - systemType - pdbFile - ligandFile - ligandCharge - minimizationSteps - equilibrationTime - productionTime properties: systemType: type: string description: "Type of system to be simulated" default: "protein" enum: - "protein" - "protein-ligand" pdbFile: type: string description: "Protein structure in pdb format to use for MD simulation (all non-protein atoms will be removed) File with extensions [pdb]" example: "9f6o.pdb" format: binary ligandFile: type: string format: binary ligandCharge: type: number description: "Charge of the ligand" minimum: -3 maximum: 3 default: 0 minimizationSteps: type: string description: "Max number of minimization steps" default: "10000" enum: - "1000" - "5000" - "10000" - "20000" - "50000" - "100000" equilibrationTime: type: number description: "" default: 0.2 productionTime: type: number description: "" default: 2 forceField: type: string description: "Choose the force field" default: "ff19SB" enum: - "ff19SB" - "ff14SB" timestep: type: string description: "Integration timestep (fs)" default: "2" enum: - "2" - "4" boxSize: type: number description: "Water padding around the solute (angstroms). Typical values: 10-15." minimum: 5 maximum: 20 default: 12 concentration: type: number description: "Ion concentration (M)" default: 0.15 temperature: type: string description: "Equilibration + production temperature (K)" default: "298" pressure: type: string description: "Equilibration + production pressure (bar)" default: "1" forceConstant: type: number description: "Force constant (kcal/mol/A²)" default: 1000 equilTrajFreq: type: string description: "Trajectory write frequency (steps)" default: "1000" enum: - "500" - "1000" - "2000" - "5000" - "10000" prodTrajFreq: type: string description: "Trajectory write frequency (steps)" default: "1000" enum: - "500" - "1000" - "2000" - "5000" - "10000" removeWaters: type: string description: "Remove waters before simulation" default: "no" enum: - "yes" - "no" stepSize: type: number description: "Step size for subsampling during 2D RMSD Generation" default: 5 # Openmm-Metadynamics Settings OpenmmMetadynamicsSettings: type: object required: - systemType - pdbFile - ligandFile - ligandCharge - minimizationSteps - equilibrationTime - productionTime - metadynamicsType - collectiveVariable1 - cv1Atoms - cv1Sigma - enableCV2 - collectiveVariable2 - cv2Atoms - cv2Sigma - gaussianHeight - gaussianPace - biasFactor - plumedOutputFreq - prodTrajFreq - previousHillsFile properties: systemType: type: string description: "Type of system to be simulated" default: "protein" enum: - "protein" - "protein-ligand" pdbFile: type: string description: "Protein structure in pdb format to use for metadynamics simulation File with extensions [pdb]" example: "9f6o.pdb" format: binary ligandFile: type: string format: binary ligandCharge: type: number description: "Charge of the ligand" minimum: -3 maximum: 3 default: 0 forceField: type: string description: "Choose the force field" default: "ff19SB" enum: - "ff19SB" - "ff14SB" boxSize: type: number description: "Water padding around the solute (angstroms). Typical values: 10-15." minimum: 5 maximum: 20 default: 12 concentration: type: number description: "Ion concentration (M)" default: 0.15 temperature: type: string description: "Simulation temperature (K)" default: "298" pressure: type: string description: "Simulation pressure (bar)" default: "1" timestep: type: string description: "Integration timestep (fs)" default: "2" enum: - "2" - "4" removeWaters: type: string description: "Remove crystallographic waters before simulation" default: "yes" enum: - "yes" - "no" minimizationSteps: type: string description: "Max number of minimization steps" default: "10000" enum: - "1000" - "5000" - "10000" - "20000" - "50000" - "100000" equilibrationTime: type: number description: "Time for equilibration phase (ns)" default: 0.2 productionTime: type: number description: "Time for metadynamics production run (ns) - typically longer than standard MD" default: 10 metadynamicsType: type: string description: "Type of metadynamics to perform" default: "well-tempered" enum: - "standard" - "well-tempered" collectiveVariable1: type: string description: "Type of first collective variable to bias" default: "rmsd" enum: - "rmsd" - "distance" - "angle" - "dihedral" - "coordination" - "gyration" cv1Atoms: type: string description: "Atom selection for first CV (e.g. 5, 1-100 / 1,5-8,10 for atoms)" cv1ReferenceFile: type: string description: "Reference PDB for RMSD calculation (if empty, uses starting structure) File with extensions [pdb]" format: binary cv1Sigma: type: number description: "Width of Gaussians for first CV (nm for distance/RMSD, radians for angles)" minimum: 0.01 maximum: 1 default: 0.05 cv1Min: type: number description: "Minimum value for CV1 grid (nm for distance/RMSD, radians for angles)" default: 0 cv1Max: type: number description: "Maximum value for CV1 grid (nm for distance/RMSD, radians for angles)" default: 1 enableCV2: type: string description: "Enable 2D metadynamics with a second CV" default: "no" enum: - "yes" - "no" collectiveVariable2: type: string description: "Type of second collective variable" default: "distance" enum: - "rmsd" - "distance" - "angle" - "dihedral" - "coordination" - "gyration" cv2Atoms: type: string description: "Atom selection for second CV" default: "" cv2Sigma: type: number description: "Width of Gaussians for second CV" minimum: 0.01 maximum: 1 default: 0.05 cv2Min: type: number description: "Minimum value for CV2 grid" default: 0 cv2Max: type: number description: "Maximum value for CV2 grid" default: 1 gaussianHeight: type: number description: "Initial height of Gaussian hills to deposit" minimum: 0.1 maximum: 10 default: 1.2 gaussianPace: type: string description: "Frequency of Gaussian deposition in MD steps" default: "500" enum: - "100" - "250" - "500" - "1000" - "2000" - "5000" - "10000" biasFactor: type: number description: "Bias factor for well-tempered metadynamics (typically 5-20, higher = more exploration)" minimum: 1 maximum: 100 default: 10 plumedOutputFreq: type: string description: "How often to write COLVAR and HILLS output" default: "500" enum: - "100" - "250" - "500" - "1000" - "2000" - "5000" prodTrajFreq: type: string description: "How often to save trajectory frames" default: "1000" enum: - "500" - "1000" - "2000" - "5000" - "10000" wallsCV1: type: string description: "Add restraining walls to keep CV1 within bounds" default: "no" enum: - "yes" - "no" wallsCV2: type: string description: "Add restraining walls to keep CV2 within bounds" default: "no" enum: - "yes" - "no" wallKappa: type: number description: "Strength of restraining walls" minimum: 10 maximum: 1000 default: 150 restartMetadynamics: type: string description: "Continue metadynamics from a previous HILLS file" default: "no" enum: - "yes" - "no" previousHillsFile: type: string description: "Upload HILLS file from previous run to continue File with extensions [dat, hills]" format: binary gridBins: type: string description: "Number of bins for free energy surface calculation" default: "100" enum: - "50" - "100" - "200" - "300" # Openmm-Relax Settings OpenmmRelaxSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure in PDB format File with extensions [pdb]" format: binary # Openmm-Temperature-Replica Settings OpenmmTemperatureReplicaSettings: type: object required: - systemType - pdbFile - ligandFile - ligandCharge - numReplicas - temperatureMin - temperatureMax - temperatureDistribution - customTemperatures - minimizationSteps - equilibrationTime - productionTime - exchangeFrequency - trajOutputFreq - energyOutputFreq - checkpointFreq - mixingStatisticsFreq - saveAllReplicas properties: systemType: type: string description: "Type of system to be simulated" default: "protein" enum: - "protein" - "protein-ligand" pdbFile: type: string description: "Protein structure in pdb format to use for replica exchange simulation File with extensions [pdb]" format: binary ligandFile: type: string format: binary ligandCharge: type: number description: "Charge of the ligand" minimum: -3 maximum: 3 default: 0 numReplicas: type: string description: "Number of replicas to simulate (typically 8-32 for T-REMD)" default: "16" enum: - "4" - "8" - "12" - "16" - "20" - "24" - "32" - "48" temperatureMin: type: number description: "Lowest temperature for replica ladder (also used for equilibration and minimization)" minimum: 273 maximum: 400 default: 298 temperatureMax: type: number description: "Highest temperature for replica ladder" minimum: 300 maximum: 500 default: 370 temperatureDistribution: type: string description: "How to distribute temperatures between replicas" default: "exponential" enum: - "linear" - "exponential" - "custom" customTemperatures: type: string description: "Comma-separated list of temperatures in Kelvin (e.g., 298,305,312,320)" default: "" minimizationSteps: type: string description: "Max number of minimization steps" default: "10000" enum: - "1000" - "5000" - "10000" - "20000" - "50000" - "100000" equilibrationTime: type: number description: "Time for equilibration phase before replica exchange (ns)" default: 0.2 productionTime: type: number description: "Total production time for replica exchange simulation (ns)" default: 10 forceField: type: string description: "Choose the force field" default: "ff19SB" enum: - "ff19SB" - "ff14SB" timestep: type: string description: "Integration timestep (fs)" default: "2" enum: - "2" - "4" friction: type: number description: "Langevin friction coefficient for temperature control (1/ps)" minimum: 0.1 maximum: 10 default: 1 boxSize: type: number description: "Water padding around the solute (angstroms). Typical values: 10-15." minimum: 5 maximum: 20 default: 12 concentration: type: number description: "Ion concentration (M)" default: 0.15 pressure: type: string description: "Simulation pressure (bar)" default: "1" barostatFrequency: type: string description: "Monte Carlo barostat frequency (steps)" default: "25" enum: - "10" - "25" - "50" - "100" forceConstant: type: number description: "Force constant for positional restraints (kcal/mol/A²)" default: 1000 removeWaters: type: string description: "Remove crystallographic waters before simulation" default: "no" enum: - "yes" - "no" exchangeFrequency: type: string description: "How often to attempt replica exchanges" default: "500" enum: - "100" - "250" - "500" - "1000" - "2000" - "5000" trajOutputFreq: type: string description: "How often to save trajectory frames for each replica" default: "1000" enum: - "500" - "1000" - "2000" - "5000" - "10000" energyOutputFreq: type: string description: "How often to write energy and state information" default: "500" enum: - "100" - "250" - "500" - "1000" - "2000" checkpointFreq: type: string description: "How often to save checkpoint files for restart capability" default: "5000" enum: - "1000" - "2000" - "5000" - "10000" - "20000" mixingStatisticsFreq: type: string description: "How often to compute and log replica exchange statistics and acceptance rates" default: "1000" enum: - "100" - "250" - "500" - "1000" - "2000" - "5000" saveAllReplicas: type: string description: "Save trajectories for all replicas or only the lowest temperature" default: "no" enum: - "yes" - "no" stepSize: type: number description: "Step size for subsampling during 2D RMSD Generation" default: 5 # Orb-Models Settings OrbModelsSettings: type: object required: - soluteSmiles - solventSmiles - weight properties: soluteSmiles: type: string solventSmiles: type: string weight: type: string # Orb-Models3 Settings OrbModels3Settings: type: object required: - proteinFile - ligandFile properties: proteinFile: type: string description: "pdb structure file for your receptor File with extensions [pdb]" example: "6w70.pdb" format: binary ligandFile: type: string description: "sdf or mol2 structure file for your ligand File with extensions [sdf, mol2]" example: "6w70_ligand.sdf" format: binary # Orthrus Settings OrthrusSettings: type: object required: - sequence properties: sequence: type: string example: "ATGATGATG" CDSPositions: type: string spliceSites: type: string # Paragraph Settings ParagraphSettings: type: object required: - proteinFile - analysisMode - heavyChain - lightChain properties: proteinFile: type: string description: "Antibody structure in PDB format. You will select chains based on the analysis mode. File with extensions [pdb]" format: binary analysisMode: type: string description: "Select which chains to analyze: paired (both heavy and light), heavy only, or light only" default: "paired" enum: - "paired" - "heavy" - "light" heavyChain: type: string description: "Select the heavy chain for the uploaded PDB file [Only available when analysisMode is one of heavy, paired]" lightChain: type: string description: "Select the light chain for the uploaded PDB file [Only available when analysisMode is one of light, paired]" # Parasurf Settings ParasurfSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Antibody pdb to predict binding site File with extensions [pdb]" example: "4N0Y_receptor_1.pdb" format: binary # Pdbsum Settings PdbsumSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Input pdb file to generate PDBSum analysis File with extensions [pdb]" example: "1a3n.pdb" format: binary # Pdockq Settings PdockqSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure file. File with extensions [pdb]" format: binary # Pepfunn Settings PepfunnSettings: type: object required: - peptide properties: peptide: type: string example: "FNCREWCWN" # Pepmlm Settings PepmlmSettings: type: object required: - targetSequence - peptideLength - numDesigns properties: targetSequence: type: string description: "Sequence of the target to design peptide against" example: "MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKE" peptideLength: type: number description: "Length of the peptide to design" default: 15 numDesigns: type: string description: "Number of designs to generate" default: 8 enum: - "1" - "2" - "4" - "8" - "16" - "32" # Peppatch Settings PeppatchSettings: type: object required: - pdbFile properties: pdbFile: type: string format: binary # Peptiverse Settings PeptiverseSettings: type: object required: - inputType - sequence - smilesInput properties: inputType: type: string description: "Select input format" default: "wt" enum: - "wt" - "smiles" sequence: type: string description: "Amino acid sequence of the peptide [Only available when inputType is one of wt]" example: "GIVEQCCTSICSLYQLENYCN" smilesInput: type: string description: "SMILES representation of the peptide/molecule [Only available when inputType is one of smiles]" example: "CC(C)C[C@@H]1NC(=O)[C@@H](CC(C)C)N(C)C(=O)[C@@H](C)N(C)C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)N(C)C(=O)[C@H]2CCCN2C1=O" targetSequence: type: string description: "Provide a target protein sequence to predict binding affinity. If left blank, binding affinity prediction is skipped." # Pka Settings PkaSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "Type of input to use File with extensions [sdf]" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string example: "CC(=O)c1ccc(O)cc1" sdfFile: type: string example: "c1cc(O)ccc1C(=O)C (Neutral Structure).sdf" format: binary # Plabdab Settings PlabdabSettings: type: object required: - task - proteinType - keywords properties: task: type: string default: "sequence" enum: - "sequence" - "keyword" proteinType: type: string default: "antibody" enum: - "antibody" - "nanobody" heavyChain: type: string description: "Protein sequence of heavy chain [Only available when task is one of sequence]" example: "VKLLEQSGAEVKKPGASVKVSCKASGYSFTSYGLHWVRQAPGQRLEWMGWISAGTGNTKYSQKFRGRVTFTRDTSATTAYMGLSSLRPEDTAVYYCARDPYGGGKSEFDYWGQGTLVTVSS" lightChain: type: string description: "Protein sequence of light chain [Only available when task is one of sequence]" example: "ELVMTQSPSSLSASVGDRVNIACRASQGISSALAWYQQKPGKAPRLLIYDASNLESGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQQFNSYPLTFGGGTKVEIKRTV" nanobodySequence: type: string example: "QVQLQESGGGLVQAGGSLRLSCAASGTISYTPDMGWYRQAPGKEREFVAGITVGTSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAASRQWGPGFYYWGQGTQVTVSS" numSamples: type: number description: "Maximum number of sequences to return [Only available when task is one of sequence]" default: 20 sortOrder: type: string description: "Criteria to sort the results. It can done by 'Heavy', 'Light' or 'Average' sequence Identity [Only available when task is one of sequence]" example: "average" default: "average" enum: - "average" - "heavy" - "light" keywords: type: string description: " PLAbDab can be searched using regular expressions for keywords contained in the title of the source literature. If searching for a specific antigen target name, not every synonym will be captured. You can use a regular expression to extend your search coverage, e.g., 'RSV|Respiratory Syncytial Virus' (no quotation marks) [Only available when task is one of keyword]" example: "RSV|Respiratory Syncytial Virus" # Placer Settings PlacerSettings: type: object required: - receptorFile - ligandCode properties: receptorFile: type: string description: "pdb structure file for your receptor and ligand together File with extensions [pdb]" example: "dnHEM1.pdb" format: binary ligandCode: type: string description: "Ligand code" example: "HEM" numSamples: type: number description: "Number of poses to generate" default: 50 mutations: type: object description: "" example: ["{'residueIdx': '32', 'chain': 'A', 'newResidue': 'TRP'}"] default: [] rankBy: type: string default: "prmsd" enum: - "prmsd" - "plddt" - "plddt_pde" predictMulti: type: boolean description: "Whether to predict for multiple ligands" default: False ligandFile: type: string description: "sdf structure file for your ligand(s) File with extensions [sdf]" format: binary # Plm-Finetune Settings PlmFinetuneSettings: type: object required: - task - baseModel - csvFile - sequenceColumn - propertyColumn properties: task: type: string default: "regression" enum: - "regression" - "classification" baseModel: type: string description: "Base model to use for finetuning" default: "facebook/esm2_t33_650M_UR50D" enum: - "facebook/esm2_t6_8M_UR50D" - "facebook/esm2_t12_35M_UR50D" - "facebook/esm2_t30_150M_UR50D" - "facebook/esm2_t33_650M_UR50D" - "facebook/esm2_t36_3B_UR50D" - "Rostlab/prot_t5_xl_uniref50" - "Rosltab/ProstT5" csvFile: type: string description: "CSV file containing your sequences and property of interest File with extensions [csv]" format: binary sequenceColumn: type: string description: "Title of sequence column" propertyColumn: type: string description: "Title of property column" epochs: type: number description: "Number of Epochs to train the model for" default: 20 learningRate: type: number description: "Learning rate for model training (default: 3e-4)" default: 0.0003 batchSize: type: number description: "Training batch size per GPU (effective batch = batch size × gradient accumulation)" default: 1 gradientAccumulation: type: number description: "Number of gradient accumulation steps (effective batch size = batch × accumulation). Recommended effective batch size: 8" default: 8 valBatchSize: type: number description: "Batch size for validation evaluation" default: 16 dropout: type: number description: "Dropout rate for the classification head (0.0 to 1.0)" default: 0.2 seed: type: number description: "Random seed for reproducibility" default: 42 deepspeed: type: boolean description: "Enable DeepSpeed optimization for large models (disable for faster training on smaller models)" default: False mixedPrecision: type: boolean description: "Enable FP16 mixed precision training for faster training and lower memory usage" default: True fullModelTraining: type: boolean description: "Train the full model instead of using LoRA (requires more memory but may improve accuracy)" default: False # Plm-Inference Settings PlmInferenceSettings: type: object required: - csvFile - sequenceColumn properties: csvFile: type: string description: "CSV with sequences to predict properties for File with extensions [csv]" format: binary sequenceColumn: type: string description: "Title of sequence column" # Pocketgen Settings PocketgenSettings: type: object required: - proteinFile - ligandFile properties: proteinFile: type: string description: "Protein structure in pdb format File with extensions [pdb]" format: binary ligandFile: type: string description: " File with extensions [sdf]" format: binary # Ppap Settings PpapSettings: type: object required: - pdbFile - receptorChains - ligandChains properties: pdbFile: type: string description: "PDB file containing protein complex File with extensions [pdb]" example: "1a4y.pdb" format: binary receptorChains: type: array items: type: string description: "Chain IDs of the receptor protein (will batch over each combination with ligand chains)" example: ["A"] ligandChains: type: array items: type: string description: "Chain IDs of the ligand protein (will batch over each combination with receptor chains)" example: ["B"] # Ppiscreenml Settings PpiscreenmlSettings: type: object required: - name - protein1Chains - protein2Chains properties: name: type: string description: "Name of a previously completed AlphaFold job on Tamarind" example: "alphafold_job_name" protein1Chains: type: string description: "Chains that make up protein 1 (separated by spaces)" example: "A B" protein2Chains: type: string description: "Chains that make up protein 2 (separated by spaces)" example: "C" # Process-Atac Settings ProcessAtacSettings: type: object required: - r1Fastq - r2Fastq properties: r1Fastq: type: string description: "First paired-end FASTQ file (Read 1) File with extensions [fastq, fastq.gz]" format: binary r2Fastq: type: string description: "Second paired-end FASTQ file (Read 2) File with extensions [fastq, fastq.gz]" format: binary sampleName: type: string description: "Optional sample name for output files" default: "sample" # Prodigy Settings ProdigySettings: type: object required: - proteinFile properties: proteinFile: type: string description: "Pdb structure file to predict ddG File with extensions [pdb]" format: binary # Profam Settings ProfamSettings: type: object required: - a3mFile properties: a3mFile: type: string description: "A3M file containing multiple sequence alignment - alignment won't be used, but ensembles will be generated from the sequences in the file and averaged File with extensions [a3m]" format: binary # Profluent-E1 Settings ProfluentE1Settings: type: object required: - task - model - sequence - mask - wildtypeSequence - mutantSequence properties: task: type: string default: "scan" enum: - "scan" - "embed" model: type: string default: "Profluent-Bio/E1-300m" enum: - "Profluent-Bio/E1-150m" - "Profluent-Bio/E1-300m" - "Profluent-Bio/E1-600m" sequence: type: string description: "Protein sequence [Only available when task is one of scan, embed, mask]" example: "AAAAAC" mask: type: string description: "Residues to mask [Only available when task is one of mask]" example: "3-5" wildtypeSequence: type: string description: "Wildtype protein sequence [Only available when task is one of score]" example: "AAAAAAC" mutantSequence: type: string description: "Mutant protein sequence [Only available when task is one of score]" example: "AAAAATC" # Progen2-Finetune Settings Progen2FinetuneSettings: type: object required: - baseModel - fastaFile properties: baseModel: type: string description: "Base model to use for finetuning" default: "hugohrban/progen2-small" enum: - "hugohrban/progen2-small" - "hugohrban/progen2-medium" - "hugohrban/progen2-large" - "hugohrban/progen2-xlarge" fastaFile: type: string description: "FASTA file containing your sequences File with extensions [fasta]" format: binary epochs: type: number description: "Number of Epochs to train the model for" default: 5 # Progen2-Inference Settings Progen2InferenceSettings: type: object required: - kSamples - temperature - maxLength - seedSequence properties: kSamples: type: number description: "Top-k sampling parameter. 0 means no top-k sampling" temperature: type: number description: "Temperature for sampling" maxLength: type: number description: "Maximum length of the generated sequence" seedSequence: type: string description: "Fixed initial part of sequence we continue the generation from" # Propka Settings PropkaSettings: type: object required: - pdbFile properties: pdbFile: type: string format: binary # Prot-T5-Embeddings Settings ProtT5EmbeddingsSettings: type: object required: - sequence properties: sequence: type: string description: "Sequence to compute embedding" example: "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIN" sequenceBatching: type: boolean description: "Batch process the input sequences" default: False sequenceBatchSize: type: number description: "Determines the number of sequences in each batch" # Protein-Design Settings ProteinDesignSettings: type: object required: - task - contig - pdbFile - numDesigns - numSequences properties: task: type: string contig: type: string pdbFile: type: string format: binary numDesigns: type: string numSequences: type: string numRecycles: type: string multimer: type: string sampleEach: type: string scoring: type: array items: type: string default: ['netsolp', 'temstapro'] enum: - "netsolp" - "temstapro" # Protein-Hunter Settings ProteinHunterSettings: type: object required: - task - targetSequence - targetCCD properties: task: type: string default: "protein-binder" enum: - "protein-binder" - "small-molecule-binder" targetSequence: type: string example: "AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALE" targetCCD: type: string example: "SAM" lengthRange: type: array items: type: string default: "90,150" numDesigns: type: integer default: 1 numCycles: type: number maximum: 100 default: 7 # Protein-Metrics Settings ProteinMetricsSettings: type: object required: - metricType - pdbFile - sequence properties: metricType: type: string default: "Single Sequence Metrics" enum: - "Single Sequence Metrics" - "Structure Metrics" pdbFile: type: string format: binary sequence: type: string # Protein-Properties Settings ProteinPropertiesSettings: type: object required: - inputType - pdbFile - sequence - heavySequence - lightSequence properties: inputType: type: string default: "Structure" enum: - "Structure" - "Sequence" pdbFile: type: string format: binary sequence: type: string heavySequence: type: string lightSequence: type: string # Protein-Scoring Settings ProteinScoringSettings: type: object required: - files properties: files: type: string example: ["pdb1.pdb", "pdb2.pdb", "pdb3.pdb"] format: binary jobNames: type: string example: ["pdb1", "pdb2", "pdb3"] scoring: type: array items: type: string description: "Scoring analysis to perform on each designed structure" default: ['netsolp', 'temstapro', 'compss-sequence'] enum: - "netsolp" - "temstapro" - "compss-sequence" - "compss-structure" # Protein-Sol Settings ProteinSolSettings: type: object required: - sequence properties: sequence: type: string description: "Protein amino acid sequence (minimum 21 residues)" example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" # Protein-Solubilization Settings ProteinSolubilizationSettings: type: object required: - pdbFile - chain - numDesigns properties: pdbFile: type: string description: "Protein structure in pdb format, should be File with extensions [pdb]" example: "1haz.pdb" format: binary chain: type: string example: "B" designedResidues: type: string description: "Residues to design in the original pdb" example: "26-32" numDesigns: type: integer description: "Number of sequences to produce" default: 1 numRecycles: type: number description: "Number of times to recycle outputs back through structure prediction process for refined results" minimum: 0 maximum: 20 default: "0" # Proteina-Complexa Settings ProteinaComplexaSettings: type: object required: - task - pdbFile - targetChains - ligandCode - ameLigands - motifAtomSpec - binderLengthRange properties: task: type: string description: "Proteina-Complexa pipeline to run" default: "protein-binder" enum: - "protein-binder" - "ligand-binder" - "motif-ligand" pdbFile: type: string description: "Target structure used for binder design. For ligand-aware modes, the ligand must already be present in the PDB file. File with extensions [pdb] [Only available when task is one of protein-binder, ligand-binder, motif-ligand]" example: {'ligand-binder': '7v11_ligand_centered.pdb', 'motif-ligand': 'M0024_1nzy_v3.pdb', 'protein-binder': 'PD-L1.pdb'} format: binary targetChains: type: array items: type: string description: "Target chain IDs to expose to Proteina-Complexa for protein binder design [Only available when task is one of protein-binder]" example: ["A"] hotspotResidues: type: object description: "Optional hotspot residues to bias the binder interface. If empty, Proteina-Complexa will design without specified hotspots. [Only available when task is one of protein-binder]" example: {'A': '37,39,49,98'} ligandCode: type: string description: "Ligand residue code to target from the input PDB [Only available when task is one of ligand-binder]" example: "OQO" ameLigands: type: string description: "Ligand residue code present in the uploaded target PDB. The selected ligand is rewritten onto chain A with the generic L:0 name at runtime. [Only available when task is one of motif-ligand]" example: "L:1" motifAtomSpec: type: string description: "Motif atom specification string using residues from the uploaded target PDB, for example 'B64: [O, C]; B86: [CB, CA, N, C]'. The selected protein motif residues are rewritten onto chain B for Proteina-Complexa at runtime. [Only available when task is one of motif-ligand]" example: "B64: [O, C]; B86: [CB, CA, N, C]; B90: [CE1, ND1, NE2, CG, CD2]; B114: [N, CA]; B137: [NE1, CD1, CE2, CG, CD2, CZ2]; B145: [OD2, CG, CB, OD1]" binderLengthRange: type: array items: type: string description: "Binder length range to sample from [Only available when task is one of protein-binder, ligand-binder, motif-ligand]" default: {'ligand-binder': '80,140', 'motif-ligand': '120,220', 'protein-binder': '70,150'} numDesigns: type: integer description: "Number of independent Proteina-Complexa jobs to launch" default: 1 # Proteinmpnn Settings ProteinmpnnSettings: type: object required: - pdbFile - designedResidues properties: pdbFile: type: string description: "Protein structure file to be designed File with extensions [pdb]" example: "9f6o.pdb" format: binary designedChains: type: array items: type: string description: "Chain IDs to be designed (rest will be fixed)" example: ["B"] designedResidues: type: object description: "Residues to design in your protein, can be ranges or individual residues" example: {'B': '26 27 28 29 30 31 32 52 53 54 55 56 95 96 97 98 99 100 101 102'} default: {} numSequences: type: number description: "Number of sequences to be generated for each protein backbone" default: 2 temperature: type: number description: "Model temperature - Suggested values 0.1, 0.15, 0.2, 0.25, 0.3. Higher values will lead to more diversity" minimum: 0 maximum: 1 default: 0.1 modelType: type: string default: "proteinmpnn" enum: - "proteinmpnn" - "ligandmpnn" - "solublempnn" - "hypermpnn" - "abmpnn" noiseLevel: type: string description: "Select from models of various noise levels (A) [Only available when modelType is one of proteinmpnn, solublempnn, hypermpnn, ligandmpnn]" default: "0.2" enum: - "0.02" - "0.1" - "0.2" - "0.3" omitAAs: type: string description: "These amino acids will be avoided when generating sequences" default: "C" verifySequences: type: string description: "Automatically perform structure prediction on generated sequences for verification" enum: - "verify-alphafold" - "verify-chai" bias_AA: type: string description: "Bias toward/against specific amino acids, as comma separated list. Example: W:3.0,P:3.0,C:3.0,A:-3.0" example: "W:3.0,P:3.0,C:3.0,A:-3.0" bias_AA_per_residue: type: string description: "Bias amino acids per residue, as dictionary. Example: {\"C1\": {\"G\": -0.3, \"C\": -2.0, \"P\": 10.8}, \"C3\": {\"P\": 10.0}, \"C5\": {\"G\": -1.3, \"P\": 10.0}, \"C7\": {\"G\": -1.3, \"P\": 10.0}}" example: "{\"C1\": {\"G\": -0.3, \"C\": -2.0, \"P\": 10.8}, \"C3\": {\"P\": 10.0}, \"C5\": {\"G\": -1.3, \"P\": 10.0}, \"C7\": {\"G\": -1.3, \"P\": 10.0}}" omit_AA_per_residue: type: string description: "Specify amino acids to exclude at specific residue positions. To force a specific amino acid, omit all others. Example: {\"A1\": \"CP\", \"A2\": \"CW\"} will prevent C,P at position A1 and C,W at position A2." example: "{\"A1\": \"CP\", \"A2\": \"CW\"}" homo_oligomer: type: number description: "Number of copies of the protein (ex. 2 for dimer, 3 for trimer, etc.)" # Proteinmpnn-Ddg Settings ProteinmpnnDdgSettings: type: object required: - pdbFile - chains properties: pdbFile: type: string example: "5TPN.pdb" format: binary chains: type: string example: "H" topK: type: number description: "Maximum number of sequences to output (sorted by logit difference)" default: "10" # Proteinmpnn-Ddg-Binder Settings ProteinmpnnDdgBinderSettings: type: object required: - pdbFile - binder_chains - receptor_chains properties: pdbFile: type: string example: "5TPN.pdb" format: binary binder_chains: type: array items: type: string example: ["H", "L"] receptor_chains: type: array items: type: string example: ["A"] # Proteinmpnn-Score Settings ProteinmpnnScoreSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Pdb to score File with extensions [pdb]" format: binary sequence: type: string description: "Sequence to score" allChains: type: boolean description: "Score all chains in the PDB file" default: True chain: type: string description: "Chain to score" # Protenix Settings ProtenixSettings: type: object required: - inputFormat - sequence properties: inputFormat: type: string default: "sequence" enum: - "sequence" - "list" sequence: type: string description: "Protein sequence (use : to specify chainbreaks for multimers) [Only available when inputFormat is one of sequence]" example: "TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK:MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM" maxLength: 2048 proteins: type: string description: "List of protein sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK", "MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM"] rnas: type: string description: "List of RNA sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["GAGAGAGAAGTCAACCAGAGAAACACACCAACCCATTGCACTCCGGG", "TTGGTGGTATATTACCTGGTACGGGGGAAACTTCGTGGTGGCCGGCCACCTGACA"] dnas: type: string description: "List of DNA sequences you want included in your complex [Only available when inputFormat is one of list]" example: ["GAGAGAGAAGTCAACCAGAGAAACACACCAACCCATTGCACTCCGGG", "TTGGTGGTATATTACCTGGTACGGGGGAAACTTCGTGGTGGCCGGCCACCTGACA"] addLigands: type: boolean description: "Add small molecule ligands to your structure prediction" default: False ligands: type: string description: "Specify your ligands (CCD_XXX for CCD codes or SMILES strings), use : to separate multiple ligands in one structure prediction (ex. CCD_ATP:CCD_MG). Each new line is a separate set of ligands, to be paired with each protein sequence. [Only available when inputFormat is one of list, sequence]" example: ["CCD_SAH", "N[C@@H](Cc1ccc(O)cc1)C(=O)O"] numSamples: type: number description: "Number of samples" maximum: 100 default: 5 numBatches: type: integer description: "Will submit multiple parallel batches with numSamples designs each" maximum: 1000 default: 1 seed: type: number description: "Random seed to use with inference" numRecycles: type: number default: 10 useTemplate: type: boolean description: "Searches PDB" default: False useGuidance: type: boolean description: "Physics-aware guidance for improved ligand plausibility (chirality, planarity, stereochemistry). Increases compute time. Most beneficial for ligand-containing predictions." default: False pocketRestraints: type: object description: "" example: ["{'binderChain': 'A', 'pocketChain': 'B', 'pocketContacts': '5 6 7'}"] default: [] contactRestraints: type: object description: "Restrain a specific residue on chain A to chain B" example: ["{'res_idxB': 1, 'chainB': 'B', 'chainA': 'A', 'res_idxA': 1}"] covalentRestraints: type: object description: "Create a covalent bond between an atom on chain A and an atom on chain B" example: ["{'res_idxB': 1, 'covalentAtomA': 'C', 'covalentAtomB': 'C', 'chainB': 'B', 'chainA': 'A', 'res_idxA': 1}"] restraintsMinDistance: type: number description: "Minimum distance for restraints" example: 0 restraintsMaxDistance: type: number description: "Maximum distance for restraints" example: 5 model: type: string description: "Select Protenix model. Use constraint model for pocket/contact restraints." default: "protenix-v2" enum: - "protenix-v2" - "protenix_base_20250630_v1.0.0" - "protenix_base_constraint_v0.5.0" - "protenix_base_default_v1.0.0" - "protenix_base_default_v0.5.0" # Proteus Settings ProteusSettings: type: object required: - csvFile - sequenceColumn - fitnessScoreColumn properties: csvFile: type: string description: "CSV file with experimental training data File with extensions [csv]" format: binary sequenceColumn: type: string fitnessScoreColumn: type: string # Protonation-State Settings ProtonationStateSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string description: "SMILES string of the molecule [Only available when inputType is one of smiles]" example: "CC(=O)Oc1ccccc1C(=O)O" sdfFile: type: string description: "SDF/MOL file File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary pH: type: number description: "pH at which to determine the dominant protonation state (e.g. 7.4 for physiological)" default: 7.4 # Psiblast Settings PsiblastSettings: type: object required: - sequence properties: sequence: type: string description: "Protein sequence to search against the PSI-BLAST database. Should contain only valid amino acid codes." example: "DVQLQESGGGLVQAGGSLRLSCAVSGQTWTNYHIGWFRQAPGKARESVASIEWGGRGTYATDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAQSSSRSPLESNYDYWGQGTQVTVSSHHHHHHHH" maxLength: 10000 database: type: string description: "Database to search against" example: "swissprot" default: "swissprot" enum: - "nr" - "swissprot" - "landmark" - "pataa" - "pdbaa" - "env_nr" - "tsa_nr" evalue: type: number description: "Expectation value threshold for BLAST search. Lower values are more stringent (0.00001-0.1)" example: "0.001" minimum: 1e-05 maximum: 0.1 default: "0.001" maxTargetSeqs: type: number description: "Maximum number of sequences to report in BLAST results (1-100)" example: "50" minimum: 1 maximum: 100 default: "50" wordSize: type: number description: "Word size for initial matches in PSI-BLAST search (2-3)" example: "3" minimum: 2 maximum: 3 default: "3" gapCosts: type: string description: "Gap opening and extension costs for PSI-BLAST alignment, separated by a space (e.g., '11 1')" example: "11 1" default: "11 1" organism: type: string description: "Filter PSI-BLAST results by organism" example: "9606" default: "" enum: - "" - "3702" - "9913" - "6239" - "3055" - "7955" - "44689" - "7227" - "562" - "3052230" - "9606" - "10090" - "2104" - "4530" - "5833" - "4754" - "10116" - "4932" - "4896" - "9823" - "31033" - "8355" - "8364" - "4577" # Pubchem Settings PubchemSettings: type: object required: - searchBy - smiles - name - pubchemId properties: searchBy: type: string description: "Select which type of input to search by" default: "SMILES" enum: - "SMILES" - "Name" - "PubChem CID" smiles: type: string description: "SMILES string to search against the PubChem database [Only available when searchBy is one of SMILES]" example: "CC(=O)Oc1ccccc1C(=O)O" maxResults: type: number description: "Maximum number of results to report (1-100) [Only available when searchBy is one of SMILES]" example: "50" minimum: 1 maximum: 100 default: "50" similarityThreshold: type: number description: "Similarity threshold for the results (0-1) [Only available when searchBy is one of SMILES]" example: "0.7" minimum: 0 maximum: 1 default: "0.7" name: type: string description: "Name of the compound to search for in the PubChem database [Only available when searchBy is one of Name]" example: "ibuprofen" pubchemId: type: string description: "PubChem CID to search for in the the PubChem database [Only available when searchBy is one of PubChem CID]" example: "3672" # Pulchra Settings PulchraSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "pdb with initial C-alpha coordinates File with extensions [pdb]" format: binary flags: type: string description: "See flags here: https://github.com/euplotes/pulchra" default: "-c -u 0.5 -b -s -z" # Pxdesign Settings PxdesignSettings: type: object required: - targetFile - targetChains - binderLength properties: targetFile: type: string description: "Target pdb to design File with extensions [pdb]" example: "1CRN.pdb" format: binary targetChains: type: array items: type: string description: "Chain IDs of target" example: ["A"] hotspots: type: object description: "Hotspots to design" example: {'A': '12-33'} binderLength: type: number description: "Length of the binder to design" default: 10 # Pykvfinder Settings PykvfinderSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure file for cavity detection File with extensions [pdb]" example: "4N0Y_receptor_1.pdb" format: binary ligandFile: type: string description: "Ligand structure to limit cavity search to region around this ligand File with extensions [pdb]" format: binary step: type: number description: "Grid step size in Ångströms. Smaller values give finer resolution but slower computation." minimum: 0.1 maximum: 2 default: 0.6 probeIn: type: number description: "Inner probe radius for cavity detection. Typically set to water molecule radius (1.4 Å)." minimum: 0.1 maximum: 5 default: 1.4 probeOut: type: number description: "Outer probe radius defining the maximum cavity opening size." minimum: 1 maximum: 10 default: 4 volumeCutoff: type: number description: "Minimum cavity volume. Cavities smaller than this are excluded from results." minimum: 0 maximum: 1000 default: 5 removalDistance: type: number description: "Distance to remove from cavity-bulk frontier for cleaner cavity boundaries." minimum: 0 maximum: 10 default: 2.4 surface: type: string description: "Surface representation: SES (Solvent Excluded Surface) or SAS (Solvent Accessible Surface)." default: "SES" enum: - "SES" - "SAS" depth: type: boolean description: "Compute cavity depth analysis to identify buried binding sites." default: True hydropathy: type: string description: "Hydrophobicity scale for mapping onto cavity surfaces. Select None to skip." default: "EisenbergWeiss" enum: - "None" - "EisenbergWeiss" - "HessaHeijne" - "KyteDoolittle" - "MoonFleming" - "RadzickaWolfenden" - "WimleyWhite" - "ZhaoLondon" ligandCutoff: type: number description: "Search radius around ligand atoms when using ligand-guided cavity detection." minimum: 1 maximum: 20 default: 5 ignoreBackbone: type: boolean description: "Exclude backbone atoms from interface residue detection." default: False plotFrequencies: type: boolean description: "Generate PDF bar chart showing residue type frequencies around each cavity." default: True # Pysca Settings PyscaSettings: type: object required: - sequence - fastaFile properties: useMSA: type: boolean description: "Generate a multiple sequence alignment using ColabFold before running SCA." default: True sequence: type: string description: "Amino acid sequence to analyze. A multiple sequence alignment will be generated automatically using ColabFold." example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCK" maxLength: 5000 fastaFile: type: string description: "Pre-computed multiple sequence alignment in FASTA format. File with extensions [fasta]" format: binary msaDatabase: type: string description: "Database to use for MSA generation." example: "uniref" default: "uniref" enum: - "uniref" - "swissprot" - "uniref+swissprot" pdbId: type: string description: "PDB ID for a reference structure to map SCA results onto. Leave blank to use the first sequence as reference." chainId: type: string description: "Chain identifier in the reference PDB structure." default: "A" precluster: type: boolean description: "Cluster sequences by identity before analysis to reduce redundancy." default: False clusterId: type: number description: "Sequence identity threshold for pre-clustering (0.5–1.0). Only used when pre-clustering is enabled." minimum: 0.5 maximum: 1 default: 0.85 doSeqcorr: type: boolean description: "Compute sequence correlations using MMseqs2." default: False doSectorId: type: boolean description: "Identify co-evolving protein sectors." default: True lbda: type: number description: "Regularization parameter lambda for SCA matrix computation. Leave blank to use the pySCA default." Ntrials: type: number description: "Number of randomization trials for sector identification. Leave blank to use the pySCA default." float32: type: boolean description: "Use 32-bit floating point precision. Reduces memory usage for large alignments." default: False # Qupkake Settings QupkakeSettings: type: object required: - inputFormat - smiles - sdfFile properties: inputFormat: type: string default: "smiles" enum: - "smiles" - "sdf" smiles: type: string example: "O=C(O)c1ccc(NC(=O)c2cn(-c3ccccc3)nc2-c2ccc(Cl)cc2)cc1" sdfFile: type: string example: "qupkake_ex.sdf" format: binary tautomerize: type: boolean description: "Find the most stable tautomer of the molecule" default: False # Rbfe Settings RbfeSettings: type: object required: - proteinPDB - networkType - ligandsSDF - atomMapper - max3d - chargeMethod - protocolRepeats - equilLength - prodLength properties: simulationType: type: string default: "rbfe" proteinPDB: type: string description: "Protein structure in pdb format File with extensions [pdb]" format: binary networkType: type: string description: "How ligands are connected in the perturbation network" default: "minimal_spanning" enum: - "minimal_spanning" - "minimal_redundant" - "star_map" - "custom" ligandsSDF: type: string description: "Ligands in sdf format File with extensions [sdf]" format: binary alchemicalNetwork: type: string description: "Interactive preview and editor for the ligand perturbation network" networkEdges: type: string atomMapper: type: string description: "Algorithm for mapping atoms between ligand pairs. Kartograf is newer and often produces better mappings for complex transformations." default: "lomap" enum: - "lomap" - "kartograf" max3d: type: number description: "Maximum 3D distance between mapped atoms in Angstroms. Lower values require better-aligned ligand poses. Increase if atom mapping fails on unaligned ligands." minimum: 0.1 maximum: 1000 default: 1 chargeMethod: type: string description: "Method for assigning partial charges to ligands. AM1-BCC is the standard method. NAGL uses a graph neural network and is faster." default: "am1bcc" enum: - "am1bcc" - "nagl" protocolRepeats: type: number description: "Number of independent repeats per transformation. Minimum 2 required for error estimation." minimum: 2 maximum: 5 default: 3 equilLength: type: number description: "Length of the equilibration phase (ps)" minimum: 0 maximum: 10000 default: 1000 prodLength: type: number description: "Length of the production phase (ps)" minimum: 0 maximum: 10000 default: 5000 # Reaction-Energy Settings ReactionEnergySettings: type: object required: - reactantSmiles - productSmiles properties: reactantSmiles: type: string description: "SMILES of reactant(s). Use . to separate multiple species (e.g. CCO.O)" example: "CCO.O" productSmiles: type: string description: "SMILES of product(s). Use . to separate multiple species (e.g. CC=O.O)" example: "CC=O.O" method: type: string description: "Level of theory. Each species is optimized and its energy computed at this level" default: "xtb-gfn2" enum: - "xtb-gfn2" - "r2scan-3c" - "b3lyp" - "wb97x-d3" basisSet: type: string description: "Basis set for DFT methods" default: "def2-svp" enum: - "def2-svp" - "def2-svpd" - "def2-tzvp" - "def2-tzvpd" solvent: type: string description: "Implicit solvation for all species in the reaction" default: "none" enum: - "none" - "water" - "acetonitrile" - "dmso" - "methanol" - "ethanol" - "chloroform" - "toluene" - "thf" - "dichloromethane" includeThermochemistry: type: boolean description: "Compute enthalpy (Delta H), entropy (Delta S), and Gibbs free energy (Delta G) via frequency analysis" default: False temperature: type: number description: "Temperature for thermochemical corrections (default 298.15 K = 25 C)" default: 298.15 # Redox Settings RedoxSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "Type of input to use File with extensions [sdf]" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string example: "CC(=O)c1ccc(O)cc1" sdfFile: type: string example: "c1cc(O)ccc1C(=O)C (Neutral Structure).sdf" format: binary # Reinvent-Finetune Settings ReinventFinetuneSettings: type: object required: - task - data - smilesCol - inferenceSmilesFile - scoringSmilesFile properties: task: type: string default: "train" enum: - "train" - "inference" - "scoring" data: type: string description: "Required if task = 'train' - list of SMILES to finetune model with File with extensions [csv] [Only available when task is one of train]" format: binary smilesCol: type: string description: "Required if task = 'train' - column in data file with SMILES strings [Only available when task is one of train]" example: "SMILES" numDesigns: type: number description: "Number of designs to generate [Only available when task is one of inference]" default: 100 modelFile: type: string description: "For custom/finetuned model inference: past training job name in format {jobName}.model, or 'reinvent.prior' for the base model. Omit to use the pretrained model for the selected modelType. [Only available when task is one of inference]" example: "pastInferenceJobName.model" modelType: type: string description: "Model type. For training, selects the prior. For inference, determines pretrained model or sampling config for custom .model files. [Only available when task is one of train, inference]" default: "reinvent" enum: - "reinvent" - "mol2mol" - "libinvent" - "linkinvent" - "pepinvent" inferenceSmilesFile: type: string description: "SMILES file for non-reinvent inference (mol2mol, libinvent, linkinvent, pepinvent). Required for both pretrained and custom model inference with these model types. File with extensions [smi] [Only available when task is one of inference]" format: binary rlSmilesFile: type: string description: "SMILES file for RL training with non-reinvent model types (mol2mol, libinvent, linkinvent, pepinvent). File with extensions [smi] [Only available when task is one of train]" format: binary scoringSmilesFile: type: string description: "Smiles file with molecules to score File with extensions [smi] [Only available when task is one of scoring]" format: binary sampleStrat: type: string description: "Sampling strategy: 'multinomial' (default) or 'beamsearch' (deterministic). Used for mol2mol and pepinvent model types. [Only available when task is one of inference]" default: "multinomial" enum: - "multinomial" - "beamsearch" temp: type: number description: "Temperature for multinomial sampling. Used for mol2mol and pepinvent model types. [Only available when task is one of inference]" default: 1 stages: type: string description: "JSON array of RL stages. Each stage: {max_steps, max_score, min_steps, termination, scoringComponents: [...]}. If omitted, falls back to flat scoringComponents in a single stage. [Only available when task is one of train]" scoringComponents: type: string description: "JSON array of scoring components, each with type, weight, and optional params (transform, low, high, k, smiles, smarts, radius, use_chirality). Available types: QED, MolecularWeight, SlogP, TPSA, TanimotoSimilarity, NumAtomStereoCenters, HBondAcceptors, HBondDonors, NumRotBond, SAScore, custom_alerts, GraphLength, Csp3, NumHeavyAtoms, NumHeteroAtoms, NumRings, NumAromaticRings, NumAliphaticRings, LargestRingSize, MolVolume, GroupCount, MatchingSubstructure. Transforms: sigmoid, reverse_sigmoid, double_sigmoid, left_step, right_step, step, exponential_decay. MatchingSubstructure supports use_chirality (boolean, default false). [Only available when task is one of train, scoring]" sigma: type: number description: "RL reward multiplier (sigma). Controls how strongly scoring influences generation vs the prior model. [Only available when task is one of train]" default: 128 diversityFilter: type: string description: "JSON object: {enabled, type, bucket_size, minscore, minsimilarity, penalty_multiplier}. Types: IdenticalMurckoScaffold, IdenticalTopologicalScaffold, ScaffoldSimilarity, PenalizeSameSmiles. [Only available when task is one of train]" inception: type: string description: "JSON object: {enabled, memory_size (default 50), sample_size (default 10), smiles_file (optional seed SMILES)}. [Only available when task is one of train]" max_steps: type: number description: "Maximum RL steps (used when stages is not provided, backward compat) [Only available when task is one of train]" default: 300 num_epochs: type: number description: "Number of epochs for fine-tuning on your training data (reinvent models only) [Only available when task is one of train]" default: 50 rate: type: number description: "Learning rate for reinforcement learning [Only available when task is one of train]" default: 0.0001 standardize_smiles: type: boolean description: "Canonicalize SMILES before fine-tuning (reinvent models only) [Only available when task is one of train]" default: True randomize_smiles: type: boolean description: "Augment training data with randomized SMILES (reinvent models only) [Only available when task is one of train]" default: True internal_diversity: type: boolean description: "Filter out duplicate molecules during fine-tuning (reinvent models only) [Only available when task is one of train]" default: False # Rf3 Settings Rf3Settings: type: object required: - inputFormat - sequence - molecules properties: inputFormat: type: string default: "sequence" enum: - "sequence" - "molecules" sequence: type: string description: "Protein sequence (use : to specify chainbreaks for multimers) [Only available when inputFormat is one of sequence]" example: "TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQIL" molecules: type: string example: ["{'type': 'protein', 'sequence': 'TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQIL', 'chain': 'A'}", "{'type': 'protein', 'sequence': 'MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM', 'chain': 'B'}", "{'inputType': 'ccd', 'chain': 'L', 'ccdCode': 'ATP', 'type': 'ligand'}"] # Rfantibody Settings RfantibodySettings: type: object required: - task - targetFile - antibodyFile - heavyChain - lightChain - antigenChain - hcdr1Residues - hcdr2Residues - hcdr3Residues - lcdr1Residues - lcdr2Residues - lcdr3Residues properties: task: type: string description: "Antibody or nanobody input" example: "nanobody" default: "antibody" enum: - "antibody" - "nanobody" framework: type: string description: "Choose from nanobody/scfv frameworks from RFantibody paper or upload your own" example: {'antibody': 'hu-4D5-8_Fv', 'nanobody': 'h-NbBCII10'} default: {'antibody': 'hu-4D5-8_Fv', 'nanobody': 'h-NbBCII10'} enum: - "custom" - "h-NbBCII10" - "hu-4D5-8_Fv" targetFile: type: string description: "Antigen pdb to target File with extensions [pdb]" example: "9f6o.pdb" format: binary antibodyFile: type: string description: "Antibody framework that we wish to use for our design. RFdiffusion will only design the structure and sequence of regions of the framework which are annotated as loops. This structure does not have to be in a bound pose. File with extensions [pdb]" example: "9f6o.pdb" format: binary heavyChain: type: string description: "ID in pdb file of heavy chain" example: "B" lightChain: type: string description: "ID in pdb file of light chain [Only available when task is one of antibody]" example: "L" antigenChain: type: string description: "ID in pdb file of the antigen chain" example: "A" hotspots: type: string description: "Residues to target" example: "305,456" default: "" regions: type: string description: "CDR Regions to design. For each region, you can specify a fixed length (ex. 10), a length range (ex. 10-15), or use 'auto' to automatically use the Chothia-defined CDR boundaries from your framework structure." example: ["hcdr1", "hcdr2", "hcdr3"] default: {'antibody': ['hcdr1', 'hcdr2', 'hcdr3', 'lcdr1', 'lcdr2', 'lcdr3'], 'nanobody': ['hcdr1', 'hcdr2', 'hcdr3']} enum: - "hcdr1" - "hcdr2" - "hcdr3" - "lcdr1" - "lcdr2" - "lcdr3" hcdr1Length: type: string description: "Length or length range for hcdr1 (ex. 5, 5-6) or auto to use the Chothia defined CDR region" default: "auto" hcdr2Length: type: string description: "Length or length range for hcdr2 (ex. 5, 5-6) or auto to use the Chothia defined CDR region" default: "auto" hcdr3Length: type: string description: "Length or length range for hcdr3 (ex. 5, 5-6) or auto to use the Chothia defined CDR region" default: "auto" lcdr1Length: type: string description: "Length or length range for lcdr1 (ex. 5, 5-6) or auto to use the Chothia defined CDR region [Only available when task is one of antibody]" default: "auto" lcdr2Length: type: string description: "Specify a fixed length (ex. 5), length range (ex. 5-6), or 'auto' to use Chothia-defined CDR boundaries from your framework [Only available when task is one of antibody]" default: "auto" lcdr3Length: type: string description: "Specify a fixed length (ex. 5), length range (ex. 5-6), or 'auto' to use Chothia-defined CDR boundaries from your framework [Only available when task is one of antibody]" default: "auto" selectCDRIndices: type: boolean description: "Select which residues are in CDRs instead of automatically detecting CDRs from your framework structure" default: False hcdr1Residues: type: string description: "Select the residues that define the HCDR1 region in your custom framework (residue numbers starting from 1)" hcdr2Residues: type: string description: "Select the residues that define the HCDR2 region in your custom framework (residue numbers starting from 1)" hcdr3Residues: type: string description: "Select the residues that define the HCDR3 region in your custom framework (residue numbers starting from 1)" lcdr1Residues: type: string description: "Select the residues that define the LCDR1 region in your custom framework (residue numbers starting from 1) [Only available when task is one of antibody]" lcdr2Residues: type: string description: "Select the residues that define the LCDR2 region in your custom framework (residue numbers starting from 1) [Only available when task is one of antibody]" lcdr3Residues: type: string description: "Select the residues that define the LCDR3 region in your custom framework (residue numbers starting from 1) [Only available when task is one of antibody]" abmpnnWeights: type: boolean description: "Use AbMPNN weights for ProteinMPNN stage" calculateEpitopeDistance: type: boolean description: "Calculate minimum distance from designed CDR loops to hotspot residues (epitope)" default: True numDesigns: type: integer description: "Number of designs to generate, for a production run, we would recommend ~10,000 in silico designs, testing at least ~100 in wet lab, ideally more 1000-10,000" default: 1 bias_AA: type: string description: "Bias toward/against specific amino acids, as comma separated list. Example: W:3.0,P:3.0,C:3.0,A:-3.0" example: "W:3.0,P:3.0,C:3.0,A:-3.0" bias_AA_per_residue: type: string description: "Bias amino acids per residue, as dictionary. Example: {\"C1\": {\"G\": -0.3, \"C\": -2.0, \"P\": 10.8}, \"C3\": {\"P\": 10.0}, \"C5\": {\"G\": -1.3, \"P\": 10.0}, \"C7\": {\"G\": -1.3, \"P\": 10.0}}" example: "{\"C1\": {\"G\": -0.3, \"C\": -2.0, \"P\": 10.8}, \"C3\": {\"P\": 10.0}, \"C5\": {\"G\": -1.3, \"P\": 10.0}, \"C7\": {\"G\": -1.3, \"P\": 10.0}}" temperature: type: number description: "Temperature for sampling in ProteinMPNN step. Higher values increase diversity" example: 0.1 default: 0.1 seqs_per_struct: type: number description: "Number of sequences to generate per structure in ProteinMPNN step" example: 1 default: 1 omit_AAs: type: string description: "Amino acids to omit during ProteinMPNN sequence generation (e.g., 'CX' to omit cysteine and unknown)" example: "CX" augment_eps: type: number description: "Data augmentation epsilon for ProteinMPNN step" example: 0.05 default: 0.05 num_connections: type: number description: "Number of connections for ProteinMPNN processing" example: 48 default: 48 n_recycles: type: number description: "Number of recycles for RF2 structure prediction step" example: 3 default: 3 n_models: type: number description: "Number of models to generate in RF2 structure prediction step" example: 5 default: 5 hotspot_percentage: type: number description: "Hotspot percentage for RF2 structure prediction step" example: 0.1 default: 0.1 # Rfdiffusion Settings RfdiffusionSettings: type: object required: - task - pdbFile - contigs - targetChains - binderLength - designedChain - designedResidues - diffusedResidues - interfaceResidues - foldConditioningTargetFile - foldConditioningBinderFile - symmetryType - oligomerLength - motifResidues - scaffoldLengthBefore - scaffoldLengthAfter properties: task: type: string default: "Motif Scaffolding" enum: - "Custom Contigs" - "Binder Design" - "Binder Redesign" - "Motif Scaffolding" - "Partial Diffusion" - "Fold Conditioning" - "Symmetric Oligomer" - "Symmetric Motif Scaffolding" pdbFile: type: string example: {'Custom Contigs': 'insulin_target.pdb', 'Binder Design': 'insulin_target.pdb', 'Binder Redesign': '9f6o.pdb', 'Partial Diffusion': '2KL8.pdb', 'Symmetric Motif Scaffolding': 'nickel_symmetric_motif.pdb', 'Motif Scaffolding': '5TPN.pdb'} format: binary contigs: type: string description: "Write contigs directly using RFdiffusion notation - see https://github.com/RosettaCommons/RFdiffusion for format details [Only available when task is one of Custom Contigs]" example: "22-22/0 A1-150" targetChains: type: array items: type: string description: "Chain IDs of target [Only available when task is one of Binder Design]" example: ["A"] binderLength: type: string description: "Length of the binder region to be designed - length (20) or range of lengths to sample uniformly (20-30) [Only available when task is one of Binder Design]" example: "20-30" binderHotspots: type: object description: "Residues to focus on on your target when designing a binder [Only available when task is one of Binder Design]" example: {'A': '20 21 23'} hotspotChain: type: string description: "Chain to select residues to focus on [Only available when task is one of Binder Redesign, Custom Contigs]" example: {'Custom Contigs': 'A', 'Binder Redesign': 'B'} hotspots: type: string description: "Residues to focus on on your target when designing a binder [Only available when task is one of Binder Redesign, Custom Contigs]" example: {'Custom Contigs': '100,101,102', 'Binder Redesign': '264,267,271'} binderChain: type: string description: "Chain ID of binder chain [Only available when task is one of Binder Redesign]" example: "B" designedChain: type: string description: "Chain ID of chain to be designed (other chains will be kept fixed) [Only available when task is one of Partial Diffusion]" example: "A" interfaceChain: type: string description: "Chain ID of chain with interface to be scaffolded [Only available when task is one of Motif Scaffolding]" example: "A" designedResidues: type: string description: "Select fixed residues and adjust the lengths of the designed regions, or write contigs directly using RFdiffusion notation [Only available when task is one of Binder Redesign]" example: "26-32,52-57,99-110" diffusedResidues: type: string description: "Select fixed residues and adjust the lengths of the designed regions, or write contigs directly using RFdiffusion notation [Only available when task is one of Partial Diffusion]" example: "1-5, 7-10" provideSeq: type: string description: "Specify residue positions that should keep their original amino acid sequence during partial diffusion (only backbone coordinates will be refined). Multiple ranges can be comma-separated. [Only available when task is one of Partial Diffusion]" example: "1-10,20-30" interfaceResidues: type: string description: "Select interface residues to be kept in your final protein. You can then select designed region lengths for 1 more than the number of contiguous interface ranges you select below. [Only available when task is one of Motif Scaffolding]" example: "30-40, 60-70" designedLengths: type: object description: "Length of the region to be designed between fixed residues - length (20) or range of lengths to sample uniformly (20-30) [Only available when task is one of Binder Redesign, Motif Scaffolding]" numDesigns: type: integer default: "1" partial_T: type: number description: "Diffuse your protein, if selected - contigs must be same length as input pdb sequence File with extensions [pdb] [Only available when task is one of Partial Diffusion]" default: 20 foldConditioningTargetFile: type: string example: "insulin_target.pdb" format: binary foldConditioningBinderFile: type: string example: "binder.pdb" format: binary targetSSFile: type: string format: binary targetAdjFile: type: string format: binary verify: type: boolean description: "Pass designs into ProteinMPNN and Alphafold to be scored automatically [Only available when task is one of Binder Design, Binder Redesign, Motif Scaffolding, Partial Diffusion, Symmetric Oligomer, Symmetric Motif Scaffolding]" default: True verifySequences: type: string description: "Automatically perform full structure prediction with MSA on generated sequences for verification [Only available when task is one of Custom Contigs, Binder Design, Binder Redesign, Motif Scaffolding, Partial Diffusion, Fold Conditioning, Symmetric Oligomer, Symmetric Motif Scaffolding]" enum: - "verify-alphafold" - "verify-chai" - "verify-boltz" noiseScaleCa: type: number description: "Denoiser's noise scale for C alpha atoms" minimum: 0 maximum: 1 default: 1 noiseScaleFrame: type: number description: "Denoiser's noise scale for frame atoms" minimum: 0 maximum: 1 default: 1 potentials: type: string description: "Potential to use. Should be a comma-separated list of potential arguments, e.g. type:binder_ROG,binderlen:100,weight:5,min_dist:15 [Only available when task is one of Custom Contigs, Binder Design, Binder Redesign, Motif Scaffolding, Partial Diffusion, Fold Conditioning]" symmetryType: type: string description: "Type of symmetry: cyclic (C2-C6), dihedral (D2-D4), or tetrahedral [Only available when task is one of Symmetric Oligomer, Symmetric Motif Scaffolding]" enum: - "c2" - "c3" - "c4" - "c5" - "c6" - "d2" - "d3" - "d4" - "tetrahedral" oligomerLength: type: number description: "Total number of residues across all chains. Must be divisible by the number of chains (C2=2, C3=3, C4=4, C5=5, C6=6, D2=4, D3=6, D4=8, tetrahedral=12) [Only available when task is one of Symmetric Oligomer]" example: 480 motifResidues: type: string description: "Comma-separated list of motif residue ranges for each symmetric copy (e.g., 'A2-4, A7-9, A12-14, A17-19' for C4). Number of ranges must match symmetry chains. [Only available when task is one of Symmetric Motif Scaffolding]" example: "A2-4, A7-9, A12-14, A17-19" scaffoldLengthBefore: type: number description: "Number of residues to design before each motif [Only available when task is one of Symmetric Motif Scaffolding]" example: 50 default: 50 scaffoldLengthAfter: type: number description: "Number of residues to design after each motif [Only available when task is one of Symmetric Motif Scaffolding]" example: 50 default: 50 useOligContacts: type: boolean description: "Enable guiding potential to encourage inter-chain contacts [Only available when task is one of Symmetric Oligomer, Symmetric Motif Scaffolding]" default: True guideScale: type: number description: "Strength of guiding potential (recommended: 2.0) [Only available when task is one of Symmetric Oligomer, Symmetric Motif Scaffolding]" default: 2 guideDecay: type: string description: "How the guiding potential effect decays over the diffusion trajectory [Only available when task is one of Symmetric Oligomer, Symmetric Motif Scaffolding]" default: "quadratic" enum: - "constant" - "linear" - "quadratic" - "cubic" model: type: string description: "Model to use in diffusion" enum: - "default" - "Complex_beta_ckpt" # Rfdiffusion-All-Atom Settings RfdiffusionAllAtomSettings: type: object required: - pdbFile - contigs - ligandCode properties: pdbFile: type: string description: "Pdb structure file to be designed - contains both protein and ligand File with extensions [pdb]" example: "1haz.pdb" format: binary contigs: type: string description: "String describing fixed and variable regions of protein, see https://www.tamarind.bio/all-atom-design to generate contigs for your task" example: "10-120,A84-87,10-120" ligandCode: type: string description: "Ligand code - must be found in your pdb structure file" example: "CYC" numDesigns: type: integer description: "Number of designs to generate (1-16)" default: 1 includeTraj: type: boolean default: True # Rfdiffusion2 Settings Rfdiffusion2Settings: type: object required: - pdbFile - ligandCode - activeSiteAtoms properties: pdbFile: type: string description: "Protein structure in pdb format File with extensions [pdb]" example: "M0584_1ldm.pdb" format: binary ligandCode: type: string description: "Ligand code" example: "NAD" contigs: type: string description: "Specify the desired scaffold length between each residue (ex. 46). Use commas to separate the active site residues and scaffold lengths (example: 46,A106-106,59,A166-166,2,A169-169,23,A193-193,46)" example: "46,A106-106,59,A166-166,2,A169-169,23,A193-193,46" contigsAsGuidepost: type: boolean description: "When true, input motif is incorporated into the protein at indices of the network's choice" default: True activeSiteAtoms: type: object description: "" example: ["{'residue': 'A106', 'atoms': 'NE,CD,CZ'}", "{'residue': 'A166', 'atoms': 'OD1,CG'}", "{'residue': 'A169', 'atoms': 'NH2,CZ'}", "{'residue': 'A193', 'atoms': 'NE2,CD2,CE1'}"] default: [] length: type: array items: type: string description: "Length of generated protein (ignored if contigs are provided)" default: "50,100" verifyLigandMpnnChai: type: boolean default: True sasaActive: type: boolean sasaRasa: type: number description: "Specify rasa of binding ligands" # Rfdiffusion3 Settings Rfdiffusion3Settings: type: object required: - task - pdbFile - jsonInputType - jsonFile - jsonConfig - binderLength - fixAtoms - unindex - classifierFreeGuidance properties: task: type: string description: "Task to perform" default: "protein-binder-design" enum: - "protein-binder-design" - "enzyme-design" - "na-binder-design" - "small-molecule-binder-design" - "json" pdbFile: type: string description: "Pdb structure file to be designed - contains both protein and ligand File with extensions [pdb] [Only available when task is one of protein-binder-design, enzyme-design, na-binder-design, small-molecule-binder-design]" example: {'na-binder-design': '5o4d.pdb', 'protein-binder-design': '1haz.pdb', 'small-molecule-binder-design': 'IAI.pdb', 'enzyme-design': 'M0255_1mg5.pdb'} format: binary jsonInputType: type: string description: "Choose whether to upload a JSON file or enter JSON config as a string [Only available when task is one of json]" default: "string" enum: - "file" - "string" jsonFile: type: string description: "Foundry-style JSON config file (see https://github.com/RosettaCommons/foundry/blob/production/models/rfd3/docs/input.md for format) File with extensions [json] [Only available when task is one of json]" format: binary jsonConfig: type: string description: "Foundry-style JSON config as a string (see https://github.com/RosettaCommons/foundry/blob/production/models/rfd3/docs/input.md for format) [Only available when task is one of json]" example: "{\"job0\": {\"dialect\": 2, \"input\": \"start.pdb\", \"contig\": \"A1-190,40-60,B1-12,6-20,A202-271\", \"is_non_loopy\": true}}" inputFiles: type: string description: "PDB/CIF files referenced in your JSON config. Files are matched based on filename. File with extensions [pdb, cif] [Only available when task is one of json]" format: binary targetChains: type: array items: type: string description: "Chain IDs of target [Only available when task is one of protein-binder-design, na-binder-design]" example: ["A"] hotspots: type: object description: "Residues to focus on on your target when designing a binder [Only available when task is one of protein-binder-design]" binderLength: type: array items: type: string description: "Range of binder length to sample from [Only available when task is one of protein-binder-design, enzyme-design, na-binder-design, small-molecule-binder-design]" default: "100,150" ligands: type: string description: "Select ligands to target from your pdb [Only available when task is one of protein-binder-design, enzyme-design, small-molecule-binder-design]" smBinderConditions: type: object description: "Specify conditioning for ligand atoms (Fixed, Buried, Exposed). [Only available when task is one of small-molecule-binder-design]" fixAtoms: type: string default: "all" enum: - "all" - "custom" fixAtomsSelection: type: object example: ["{'selection': 'ND2,CG', 'residue': 'A108'}", "{'selection': 'OG,CB,CA', 'residue': 'A139'}", "{'selection': 'OH,CZ', 'residue': 'A152'}", "{'selection': 'NZ,CE,CD', 'residue': 'A156'}", "{'selection': 'OXT', 'residue': 'ACT'}", "{'selection': '', 'residue': 'NAI'}"] unindex: type: string description: "Whether residue index be inferred by the model instead of prespecified (all by default or comma seperated list of residues e.g. A109,A114) [Only available when task is one of enzyme-design]" default: "all" classifierFreeGuidance: type: boolean description: "Enables classifier-free guidance to strictly enforce motif adherence. Increases computational cost by 2x. [Only available when task is one of enzyme-design]" default: False oriToken: type: string description: "[x,y,z] origin override to control center of mass placement [Only available when task is one of na-binder-design]" numDesigns: type: integer description: "Number of designs to generate" default: 1 nonLoopy: type: boolean description: "Encourages the model to make more structured designs (recommended) [Only available when task is one of protein-binder-design]" default: True stepScale: type: number description: "Controls the diffusion update size. The default (1.5) promotes stable, idealized, and 'designable' structures. Lowering towards 1.0 reduces helical bias, increasing diversity. Increasing (>1.5) forces stricter convergence." minimum: 1 maximum: 5 default: 1.5 gammaZero: type: number description: "Controls how much extra noise is injected into the structure at every step of the reverse diffusion process. Decreasing tends to increase designability and decrease diversity." minimum: 0 maximum: 1 default: 0.6 # Rfpeptides Settings RfpeptidesSettings: type: object required: - pdbFile - binderLength properties: pdbFile: type: string example: "7zkr_GABARAP.pdb" format: binary targetChains: type: array items: type: string description: "Chain IDs of target" example: ["A"] binderLength: type: string description: "Length of the binder region to be designed - length (10) or range of lengths to sample uniformly (12-18)" example: "12-18" default: "12-18" binderHotspots: type: object description: "Residues to focus on on your target when designing a binder" example: {'A': '48 50 51 52 62 65'} rosetta: type: boolean description: "Get in touch at info@tamarind.bio if you have a license and would like to use RFpeptides with Rosetta" default: False numDesigns: type: integer default: "1" temperature: type: number description: "Temperature for sampling" default: 50 verify: type: boolean # Rhodesign Settings RhodesignSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "RNA 3D structure file (PDB format) File with extensions [pdb]" example: "2zh6_B.pdb" format: binary ssFile: type: string description: "Secondary structure contact map as NumPy array (.npy). If provided, enables higher-accuracy design using 2D structural information. File with extensions [npy]" format: binary temperature: type: number description: "Sampling temperature. Lower values produce more conserved sequences; higher values increase diversity." default: 1 numDesigns: type: integer description: "Number of designs to generate" default: 1 # Ribodiffusion Settings RibodiffusionSettings: type: object required: - pdbFile - numDesigns properties: pdbFile: type: string description: "RNA 3D structure used as the conditioning backbone for inverse folding File with extensions [pdb]" example: "R1107.pdb" format: binary numDesigns: type: integer description: "Launches multiple jobs when greater than 1; each job generates one design" default: 1 modelVariant: type: string description: "Optional checkpoint variant for advanced usage" default: "standard" enum: - "standard" - "full-data-noisy" condScale: type: number description: "Conditional scaling weight. w=1 emphasizes sequence recovery; lower values increase diversity (paper reports diversity gains around w=0.5)" minimum: 0 maximum: 1 dynamicThreshold: type: boolean description: "Enable percentile-based clipping and rescaling of denoised predictions during sampling to reduce extreme values and improve stability" default: False # Riffdiff Settings RiffdiffSettings: type: object required: - pdbFile - resnums - ligands properties: pdbFile: type: string description: "Theozyme input in pdb format File with extensions [pdb]" format: binary resnums: type: string description: "List of all active site residues with chain information that should be present in the catalytic motif separated by a space (e.g. A121 A153 A162)" example: "A121 A153 A162" ligands: type: string description: "List of all ligand residues with chain information that should be present in the catalytic motif (separated by a space if multiple) (e.g. A198)" example: "A198" # Rmsd-Calculator Settings RmsdCalculatorSettings: type: object required: - pdbFile1 - pdbFile2 - rmsdType - alignChains1 - rmsdChains1 - rmsdLigand1 - alignChains2 - rmsdLigand2 - rmsdChains2 properties: pdbFile1: type: string description: "Protein structure 1 in pdb format File with extensions [pdb]" example: "1a3n.pdb" format: binary pdbFile2: type: string description: "Protein structure 2 in pdb format File with extensions [pdb]" example: "PDB2.pdb" format: binary rmsdType: type: string default: "protein" enum: - "protein" - "ligand" specifyChains: type: boolean description: "Whether to specify chains to align on and compute RMSD on" default: False alignChains1: type: array items: type: string description: "Chains to align on" rmsdChains1: type: array items: type: string description: "Chains to compute RMSD on" rmsdLigand1: type: string description: "Ligand code to compute RMSD on" alignChains2: type: array items: type: string description: "Chains to align on" rmsdLigand2: type: string description: "Ligand code to compute RMSD on" rmsdChains2: type: array items: type: string description: "Chains to compute RMSD on" # Rna-Fm Settings RnaFmSettings: type: object required: - task - sequence - backbone - saveEmbeddingsFormat - visualize properties: task: type: string description: "Select the specific analysis task" default: "extract_embedding" enum: - "extract_embedding" - "ss_prediction" sequence: type: string description: "Input RNA sequence (U instead of T). For mRNA-FM, length must be divisible by 3." example: "GGGUGCGAUCAUACCAGCACUAAUGCCCUCCUGGGAAGUCCUCGUGUUGCACCC" backbone: type: string description: "Select the foundation model variant [Only available when task is one of extract_embedding]" default: "rna-fm" enum: - "rna-fm" - "mrna-fm" saveEmbeddingsFormat: type: string description: "Choose how to extract or aggregate the embeddings [Only available when task is one of extract_embedding]" default: "raw" enum: - "raw" - "mean" - "bos" visualize: type: boolean description: "Generate PNG visualizations of the predicted secondary structure, including a 2D forgi plot, arc diagram, contact heatmap, and linear dot-bracket view. [Only available when task is one of ss_prediction]" default: False # Rog Settings RogSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure in pdb format File with extensions [pdb]" example: "1a3n.pdb" format: binary # Rosetta-Ddg-Prediction Settings RosettaDdgPredictionSettings: type: object required: - pdbFile - saturationMutagenesis - mutations - positions - residueTypes properties: pdbFile: type: string description: "PDB structure to mutate File with extensions [pdb]" example: "1a3n.pdb" format: binary saturationMutagenesis: type: boolean description: "Whether or not to perform saturation mutagenesis scan on selected positions" default: False mutations: type: string description: "Mutations (in the format of chain.wt_residue.position.mutant_residue) to predict. Mutations should be newline-separated, with multiple simultaneous mutations provided on the same line and separated by a comma. For flexddg, each line should also specify the chain to be moved away from the complex when scoring each chain of the complex separately to compute the ddG of binding. This chain should be specified at the end of each line with a semicolon separating the mutation and the chain." example: ["A.V.1.K"] positions: type: string description: "Mutation positions (in the format of chain.wt_residue.position) to scan. Mutation positions should be newline-separated, with multiple simultaneous mutations provided on the same line and separated by a comma. For flexddg, each line should also specify the chain to be moved away from the complex during scoring. This chain should be specified at the end of each line with a semicolon separating the mutation position and the chain." example: ["A.V.1"] residueTypes: type: string description: "Residues types (formatted in the one-letter convention for the 20 canonical residues) that will be part of the scan. Residue types should be newline-separated." example: ["A"] protocol: type: string description: "Protocol to use for prediction" default: "cartddg2020" enum: - "cartddg2020" - "cartddg" - "flexddg" energyFunction: type: string description: "Energy function used by the protocol" default: "ref2015" enum: - "ref2015" - "talaris2014" iterations: type: number description: "Number of iterations of refinement for cartddg/cartddg2020 (ignored for flexddg)" minimum: 1 maximum: 10 default: 5 nstruct: type: number description: "Number of structures to be generated for each mutation" minimum: 1 maximum: 100 default: 35 numBackrubTrials: type: number description: "Number of backrub trials" minimum: 1000 maximum: 100000 default: 35000 backrubTrajStride: type: number description: "Backrub trajectory stride" minimum: 1000 maximum: 10000 default: 7000 maxMinimizationIterations: type: number default: 5000 maxAbsScoreConvergenceThreshold: type: number default: 1 # Rosetta-Dock Settings RosettaDockSettings: type: object required: - dockedProteinLigandFile - relaxedApoProteinFile - paramsFiles - conformersFiles - distanceConstraints properties: dockedProteinLigandFile: type: string description: "pdb structure file for your complex File with extensions [pdb]" format: binary relaxedApoProteinFile: type: string description: "pdb structure file for your receptor File with extensions [pdb]" format: binary paramsFiles: type: string description: "params files to be included in docking File with extensions [params]" format: binary conformersFiles: type: string description: "conformers files to be included in docking File with extensions [pdb]" format: binary distanceConstraints: type: string description: "distance constraints to be used in docking File with extensions [constraints]" format: binary nstruct: type: integer description: "Number of poses to generate" default: 1 # Rosetta-Fixbb Settings RosettaFixbbSettings: type: object required: - pdbFile - chain - mutResidues properties: pdbFile: type: string description: "Structure to mutate File with extensions [pdb]" format: binary chain: type: string description: "Chain ID to be designed" example: "A" mutResidues: type: string description: "Residue numbers to mutate" example: "46 47 48 49 50 51 52 53 56 57 60 62 63 64 65 66 105 106 108 109 110 111 112 118 119 120 121 122 123 124 125 126 129 130 159 160 161 162 163 164 165 166 169 171 172 173 174 175 176 177 178 179 198 208 212 213 214 215 216 217 218 219 226 227 228 229 230 231 232 233 234 235 255 269 270 271 272 273 274 275 276 277 278 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 301 302" numDesigns: type: number description: "Number of designs to generate" default: 5 ligandName: type: string description: "Ligand Name" example: "LIG" ligandFile: type: string description: "Conformers for ligand, separated by TER File with extensions [mol2]" format: binary conformerLibrary: type: string description: "Conformer library file with pdb rotamers File with extensions [pdb]" format: binary constraintsFile: type: string format: binary extraFlags: type: string description: "Additional flags for Rosetta" default: "" # Rosetta-Ppi Settings RosettaPpiSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Complex Structure File with extensions [pdb]" format: binary packSeparated: type: boolean description: "Repack the exposed interfaces when calculating binding energy? Usually a good idea." default: True packInput: type: boolean description: "Prepack before separating chains when calculating binding energy? Useful if these are non-Rosetta inputs." default: True customPackInputs: type: string description: "Optional custom file with input packing options for InterfaceAnalyzer. If not provided, default options will be used. File with extensions [txt]" format: binary cyclic: type: boolean description: "Whether to make the shortest chain in your complex cyclic" default: False # Rosetta-Relax Settings RosettaRelaxSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Input pdb structure to be relaxed File with extensions [pdb]" format: binary nstruct: type: integer description: "Number of poses to generate" default: 1 # Rosetta-Relax-Ligand Settings RosettaRelaxLigandSettings: type: object required: - pdbFile - molFiles properties: pdbFile: type: string description: "Input pdb structure to be relaxed File with extensions [pdb]" format: binary molFiles: type: string description: "Input mol2 ligands to be relaxed File with extensions [mol2]" format: binary paramFiles: type: string description: "Input parameters File with extensions [params]" format: binary constraints: type: string description: "Constraints for complex File with extensions [cts]" format: binary nstruct: type: integer description: "Number of poses to generate" default: 1 # Rosetta-Score Settings RosettaScoreSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Structure to score File with extensions [pdb]" format: binary # Roshambo Settings RoshamboSettings: type: object required: - queryFile - datasetFile properties: queryFile: type: string description: "SDF file with the reference molecule to compare against File with extensions [sdf]" example: "roshambo_query.sdf" format: binary datasetFile: type: string description: "SDF file with molecules to compare to the query File with extensions [sdf]" example: "roshambo_dataset.sdf" format: binary numConfs: type: number description: "Number of conformers to generate per molecule (0 = use input conformations)" default: 0 color: type: boolean description: "Include pharmacophoric feature (color) similarity in addition to shape" default: True ignoreHs: type: boolean description: "Exclude hydrogen atoms from shape comparison" default: True sortBy: type: string description: "Similarity metric used to rank results" default: "ComboTanimoto" enum: - "ComboTanimoto" - "ShapeTanimoto" - "ColorTanimoto" # Rso Settings RsoSettings: type: object required: - pdbFile - chain properties: pdbFile: type: string description: "Target pdb to design File with extensions [pdb]" format: binary chain: type: string description: "For PDB targets, protein and DNA/RNA enter target chain ID" example: "A" numDesigns: type: number description: "Number of binders to generate" default: 1 trajIters: type: number description: "Number of steps for each binder" default: 100 binderLen: type: number description: "Length for generated binders" default: 100 # Saprot Settings SaprotSettings: type: object required: - inputType - properties - sequence - pdbFile properties: inputType: type: string description: "Input type" default: "structure" enum: - "sequence" - "structure" properties: type: string example: ["solubility", "stability"] enum: - "solubility" - "stability" sequence: type: string example: "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV" pdbFile: type: string description: "Protein structure file to score File with extensions [pdb] [Only available when inputType is one of structure]" format: binary # Saprot-Finetune Settings SaprotFinetuneSettings: type: object required: - baseModel - csvFile - sequenceColumn - propertyColumn properties: baseModel: type: string description: "Base model to use for finetuning" enum: - "Official pretrained SaProt (35M)" - "Official pretrained SaProt (650M)" epochs: type: number description: "Number of Epochs to train the model for" default: 20 learningRate: type: number description: "Model learning rate" default: 0.001 csvFile: type: string description: "CSV file containing your sequences and property of interest File with extensions [csv]" format: binary sequenceColumn: type: string description: "Title of sequence column" propertyColumn: type: string description: "Title of property column" # Search-Conformations Settings SearchConformationsSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "Type of input to use File with extensions [sdf]" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string example: "CC(=O)c1ccc(O)cc1" sdfFile: type: string example: "c1cc(O)ccc1C(=O)C (Neutral Structure).sdf" format: binary # Single-Point-Energy Settings SinglePointEnergySettings: type: object required: - inputType - smiles - sdfFile - xyzFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" - "xyz" smiles: type: string description: "SMILES string of the molecule [Only available when inputType is one of smiles]" example: "CCO" sdfFile: type: string description: "SDF/MOL file with 3D coordinates File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary xyzFile: type: string description: "XYZ coordinate file (e.g. from a previous geometry optimization) File with extensions [xyz] [Only available when inputType is one of xyz]" format: binary method: type: string description: "xtb-gfn2: fast semiempirical (~10s). g-xtb: next-gen semiempirical approximating wB97M-V/def2-TZVPPD (~1min). r2scan-3c: composite DFT (~3min). b3lyp/wb97x-d3: full DFT (~10-30min)" default: "xtb-gfn2" enum: - "xtb-gfn2" - "g-xtb" - "r2scan-3c" - "b3lyp" - "wb97x-d3" basisSet: type: string description: "Basis set size controls accuracy vs. speed. Use -d (diffuse) variants for anions. Larger basis = more accurate but slower" default: "def2-svp" enum: - "def2-svp" - "def2-svpd" - "def2-tzvp" - "def2-tzvpd" - "def2-qzvp" - "6-31g*" - "cc-pvdz" - "cc-pvtz" charge: type: number description: "Net molecular charge (e.g. 0 for neutral, -1 for anion, +1 for cation)" default: 0 multiplicity: type: number description: "Spin multiplicity (2S+1). Use 1 for closed-shell singlet, 2 for doublet radical, 3 for triplet" default: 1 solvent: type: string description: "Implicit solvation environment. 'none' computes gas-phase energy" default: "none" enum: - "none" - "water" - "acetonitrile" - "dmso" - "methanol" - "ethanol" - "chloroform" - "toluene" - "thf" - "dichloromethane" preOptimize: type: boolean description: "Run a fast xTB geometry optimization before the single point calculation. Recommended for SMILES input" default: True # Smina Settings SminaSettings: type: object required: - proteinFile - ligandFile - boxX - boxY - boxZ - width - height - depth properties: proteinFile: type: string example: "1iep.pdb" format: binary ligandFile: type: string description: "sdf structure file for your ligand (one ligand per file) File with extensions [sdf]" example: "Conformer3D_COMPOUND_CID_5291.sdf" format: binary boxX: type: number description: "X coordinate of bounding box center" example: "15.190" default: 35 boxY: type: number description: "Y coordinate of bounding box center" example: "53.903" default: 27 boxZ: type: number description: "Z coordinate of bounding box center" example: "16.917" default: 35 width: type: number description: "Width of bounding box" example: "20" default: 20 height: type: number description: "Height of bounding box" example: "20" default: 20 depth: type: number description: "Depth of bounding box" example: "20" default: 20 # Space2 Settings Space2Settings: type: object required: - proteinFiles properties: proteinFiles: type: string description: "IMGT numbered pdb file with 'H' for heavy chain ID and 'L' for light chain ID File with extensions [pdb]" format: binary cutoff: type: number description: "Clustering cutoff (A)" default: 1.24 clusteringAlgorithm: type: string description: "Clustering method - agglomerative is bottom-up, greedy makes best choi" default: "Agglomerative clustering" enum: - "Agglomerative clustering" - "Greedy clustering" CDRs: type: string description: "CDRs to use in clustering" example: ["CDRH3", "CDRL3"] enum: - "CDRH1" - "CDRH2" - "CDRH3" - "CDRL1" - "CDRL2" - "CDRL3" fw: type: string description: "Framework regions to use in clustering" example: ["fwH"] enum: - "fwH" - "fwL" heavyChain: type: string description: "Heavy chain ID to use in clustering" default: "H" lightChain: type: string description: "Light chain ID to use in clustering" default: "L" # Spatial-Ppi Settings SpatialPpiSettings: type: object required: - inputFormat - proteinA - proteinB - sequenceA - sequenceB properties: inputFormat: type: string default: "pdb" enum: - "pdb" - "sequence" proteinA: type: string description: "pdb structure file for first protein File with extensions [pdb] [Only available when inputFormat is one of pdb]" format: binary proteinAChain: type: string description: "Chain in protein A, if empty - first chain is used [Only available when inputFormat is one of pdb]" example: "A" proteinB: type: string description: "pdb structure file for your ligand File with extensions [pdb] [Only available when inputFormat is one of pdb]" format: binary proteinBChain: type: string description: "Chain in protein B, if empty - first chain is used [Only available when inputFormat is one of pdb]" example: "A" sequenceA: type: string example: "TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK:MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM" sequenceB: type: string example: "TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK:MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM" # Spin-State-Energies Settings SpinStateEnergiesSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "Type of input to use File with extensions [sdf]" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string example: "CC(=O)c1ccc(O)cc1" sdfFile: type: string example: "c1cc(O)ccc1C(=O)C (Neutral Structure).sdf" format: binary # Stabddg Settings StabddgSettings: type: object required: - pdbFile - binder1Chains - binder2Chains - mutations properties: pdbFile: type: string description: "Wild-type complex PDB file File with extensions [pdb]" example: "1AO7.pdb" format: binary binder1Chains: type: array items: type: string description: "Chain IDs making up the first binder of the interface" example: ["A", "B", "C"] binder2Chains: type: array items: type: string description: "Chain IDs making up the second binder of the interface" example: ["D", "E"] mutations: type: string description: "Mutations to evaluate, in the format wildtype+chain+position+mutant (e.g., EA63Q = E to Q at position 63 of chain A). Use the residue numbering from your submitted PDB — StaB-ddG requires each chain to start at residue 1, so the PDB and mutation positions are automatically renumbered before inference (the renumbered mutation string is reported alongside the result). One entry per line; for multi-point mutants on a single entry, separate individual mutations with commas (e.g., \"EA63Q,QD30V,KA66A\")." example: ["EA63Q,QD30V,KA66A"] mcSamples: type: number description: "Number of Monte Carlo samples to average over for variance reduction (default 20)." default: 20 seed: type: number description: "Seed for reproducibility. Leave blank to use a random seed." # Structural-Evolution Settings StructuralEvolutionSettings: type: object required: - pdbFile - chain properties: pdbFile: type: string description: "Pdb structure file of the protein or protein complex (must be numbered 1..n) File with extensions [pdb]" format: binary chain: type: string description: "Target chain you wish to evolve" example: "A" upperLimit: type: number description: "Number of residues to consider for mutation, e.g. mutations will be recommended in the residue indices in the range 1 to selected upper limit." example: 10 # Superwater Settings SuperwaterSettings: type: object required: - pdbFile properties: pdbFile: type: string description: "Protein structure in pdb format to add waters to File with extensions [pdb]" example: "1iep.pdb" format: binary waterRatio: type: number description: "Number of water molecules predicted by the diffusion model" minimum: 1 maximum: 20 default: 15 cap: type: number description: "Probability cutoff for water molecule sampling (higher values increase precision but reduce coverage)" minimum: 0.02 maximum: 0.5 default: 0.1 # Surfdock Settings SurfdockSettings: type: object required: - proteinFile - ligandFormat - ligandFile - ligandSmiles properties: proteinFile: type: string description: "pdb structure file for your receptor File with extensions [pdb]" example: "6w70.pdb" format: binary ligandFormat: type: string description: "Choose the format of your ligand input" default: "sdf file" enum: - "sdf file" - "SMILES" ligandFile: type: string description: "sdf structure file for your ligand File with extensions [sdf]" example: "6w70_ligand.sdf" format: binary ligandSmiles: type: string description: "SMILES string for your ligand" numSamples: type: number description: "Number of docked poses to generate" default: 40 # Syn-Codon-Lm Settings SynCodonLmSettings: type: object required: - task - sequence - species properties: task: type: string default: "embeddings" enum: - "embeddings" - "optimize" sequence: type: string example: {'embeddings': 'ATGTCCACCGGGCGGTGA', 'optimize': 'MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFGYGL'} species: type: string default: "E. coli" enum: - "E. coli" - "S. cerevisiae" - "M. musculus" - "H. sapiens" customSpecies: type: number description: "If your desired organism is not found above, select your species code from this list: https://github.com/Boehringer-Ingelheim/SynCodonLM/blob/master/SynCodonLM/species_token_type.py. If specified, species will be ignored. " minimum: 0 maximum: 499 # Tap Settings TapSettings: type: object required: - heavySequence - lightSequence properties: heavySequence: type: string description: "Heavy sequence of your antibody" example: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" lightSequence: type: string description: "Light sequence of your antibody" example: "QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIN" # Tautomer Settings TautomerSettings: type: object required: - inputType - smiles - sdfFile properties: inputType: type: string description: "Type of input to use File with extensions [sdf]" default: "smiles" enum: - "smiles" - "sdf" smiles: type: string example: "CC(=O)c1ccc(O)cc1" sdfFile: type: string example: "c1cc(O)ccc1C(=O)C (Neutral Structure).sdf" format: binary # Tcrmodel2 Settings Tcrmodel2Settings: type: object required: - type - A - B - peptide - MHCA - MHCB properties: type: type: string default: "class1" enum: - "class1" - "class2" - "unbound" A: type: string example: {'class2': 'LAKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEVASLFIPADRKSSTLSLPRVSLSDTAVYYCLVGDTGFQKLVFGTGTRLLVSP', 'class1': 'AQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTNQAGTALIFGKGTTLSVSS', 'unbound': 'AQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTNQAGTALIFGKGTTLSVSS'} B: type: string example: {'class2': 'GAVVSQHPSWVICKSGTSVKIECRSLDFQATTMFWYRQFPKQSLMLMATSNEGSKATYEQGVEKDKFLINHASLTLSTLTVTSAHPEDSSFYICSARDPGGGGSSYEQYFGPGTRLTVT', 'class1': 'NAGVTQTPKFQVLKTGQSMTLQCSQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYSIRGSRGEQFFGPGTRLTVL', 'unbound': 'NAGVTQTPKFQVLKTGQSMTLQCSQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYSIRGSRGEQFFGPGTRLTVL'} peptide: type: string example: {'class2': 'LAWEWWRTV', 'class1': 'RLPAKAPLL'} MHCA: type: string example: {'class2': 'IKADHVSTYAAFVQTHRPTGEFMFEFDEDEMFYVDLDKKETVWHLEEFGQAFSFEAQGGLANIAILNNNLNTLIQRSNHTQAT', 'class1': 'SHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDGKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLH'} MHCB: type: string example: "PENYLFQGRQECYAFNGTQRFLERYIYNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTLQR" # Td-Dft Settings TdDftSettings: type: object required: - inputType - smiles - sdfFile - xyzFile properties: inputType: type: string description: "How to provide your molecule" default: "smiles" enum: - "smiles" - "sdf" - "xyz" smiles: type: string description: "SMILES string of the molecule (e.g. naphthalene) [Only available when inputType is one of smiles]" example: "c1ccc2ccccc2c1" sdfFile: type: string description: "SDF/MOL file with 3D coordinates File with extensions [sdf] [Only available when inputType is one of sdf]" format: binary xyzFile: type: string description: "Pre-optimized XYZ coordinate file File with extensions [xyz] [Only available when inputType is one of xyz]" format: binary method: type: string description: "b3lyp: standard. cam-b3lyp: better for charge-transfer excitations. wb97x-d3: general purpose. pbe0: fast" default: "b3lyp" enum: - "b3lyp" - "cam-b3lyp" - "wb97x-d3" - "pbe0" basisSet: type: string description: "Basis set for the excited-state calculation. Diffuse functions (+, -d) improve Rydberg/CT states" default: "def2-svp" enum: - "def2-svp" - "def2-svpd" - "def2-tzvp" - "def2-tzvpd" - "6-31+g*" charge: type: number description: "Net molecular charge" default: 0 multiplicity: type: number description: "Spin multiplicity (2S+1)" default: 1 solvent: type: string description: "Implicit solvation shifts absorption wavelengths (solvatochromism)" default: "none" enum: - "none" - "water" - "acetonitrile" - "dmso" - "methanol" - "ethanol" - "chloroform" - "toluene" - "thf" - "dichloromethane" numStates: type: number description: "How many excited states to compute. More states = broader spectral coverage but slower" default: 10 tda: type: boolean description: "TDA is ~2x faster with minimal accuracy loss for most absorption spectra" default: False preOptimize: type: boolean description: "Optimize geometry with xTB before the TD-DFT calculation" default: True # Tempro Settings TemproSettings: type: object required: - sequence properties: sequence: type: string description: "Nanobody melting temperature" example: "QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS" # Temstapro Settings TemstaproSettings: type: object required: - sequence properties: sequence: type: string description: "Protein sequence to assess thermostability" example: "AKLAGQKVRIGGWVKTGRQQGKGTFAFLEVNDGSCPANLQVMVDSSLYDLSRLVATGTCVTVDGVLKIPPEGKGLKQSIELSVETVIAVGTVDP" # Thermompnn Settings ThermompnnSettings: type: object required: - pdbFile - chains properties: pdbFile: type: string description: "Protein structure file to be designed File with extensions [pdb]" example: "3HTN.pdb" format: binary allChains: type: boolean default: False chains: type: array items: type: string description: "Chain IDs to be designed" example: ["A"] verify: type: boolean description: "Automatically perform structure prediction on generated sequences for verification" default: False topK: type: number description: "Maximum number of sequences to output (sorted by ddG)" default: "10" # Thermompnn-D Settings ThermompnnDSettings: type: object required: - pdbFile - chains - model properties: pdbFile: type: string description: "Protein structure file to be designed File with extensions [pdb]" example: "3HTN.pdb" format: binary chains: type: array items: type: string description: "Chains to use (default is all chains)" example: ["A"] model: type: string description: "Epistatic: This model attempts to capture epistatic interactions between double mutations, which requires running inference on every individual mutation | Additive: This sums the individual contributions from each single mutation without attempting to quantify epistatic coupling terms." default: "epistatic" enum: - "epistatic" - "additive" - "single" threshold: type: number description: "Threshold for SSM sweep. By default, ThermoMPNN only saves mutations below this threshold (-0.5 kcal/mol). To save all mutations, set this really high (e.g., 100)" default: -0.5 distance: type: number description: "Filter for double mutant predictions using pairwise Ca distance cutoff (default is 5 A)" default: 5 batchSize: type: number description: "Batch size for stability prediction module" default: 256 ssPenalty: type: boolean description: "Add explicit disulfide breakage penalty" default: False # Tlimmuno Settings TlimmunoSettings: type: object required: - sequence - hlas properties: sequence: type: string description: "Sequence to predict immunogenicity - if your sequence is longer than Peptide length (15 by default), we will predict immunogenicity for each sliding window peptide." example: "GLLFRRLTSREVLLL" hlas: type: string description: "HLA alleles to predict immunogenicity for" example: ["DRB1_0803"] default: ['DRB1_0803', 'DRB1_1501', 'DRB1_1101', 'DRB1_0401', 'DRB1_0301', 'DRB1_1103', 'DRB1_1303', 'DRB1_0101', 'HLA-DPA10103-DPB10301', 'DRB1_0405', 'HLA-DQA10102-DQB10502', 'DRB3_0101', 'DRB1_1301', 'DRB1_0103', 'DRB1_0402', 'DRB1_0404', 'DRB1_0901', 'DRB3_0202', 'HLA-DQA10102-DQB10602', 'DRB5_0101', 'DRB5_0202', 'DRB1_0801', 'DRB4_0103', 'DRB1_0701', 'DRB1_1001', 'DRB1_0102', 'DRB1_0818', 'DRB1_1302', 'DRB1_0406', 'DRB1_0302', 'DRB1_1102', 'HLA-DPA10103-DPB10201', 'DRB1_1502', 'DRB1_1202', 'DRB4_0101', 'HLA-DQA10301-DQB10302', 'HLA-DPA10103-DPB10401', 'HLA-DQA10501-DQB10201', 'DRB1_0403', 'DRB1_0802', 'DRB1_1404', 'DRB1_1506', 'HLA-DQA10103-DQB10603', 'DRB1_1104', 'DRB3_0301', 'DRB1_0407', 'DRB1_1406', 'DRB1_1402', 'DRB1_1201', 'DRB1_1304', 'HLA-DPA10103-DPB10402', 'HLA-DQA10401-DQB10402', 'DRB1_1602', 'DRB1_1503', 'HLA-DQA10501-DQB10301', 'HLA-DQA10101-DQB10501', 'DRB1_0411', 'DRB1_1454', 'DRB5_0102', 'HLA-DPA10201-DPB11401', 'HLA-DQA10505-DQB10301', 'HLA-DQA10201-DQB10202', 'HLA-DPA10103-DPB10601', 'HLA-DQA10201-DQB10303', 'HLA-DPA10201-DPB10101', 'DRB1_0303'] enum: - "DRB1_0803" - "DRB1_1501" - "DRB1_1101" - "DRB1_0401" - "DRB1_0301" - "DRB1_1103" - "DRB1_1303" - "DRB1_0101" - "HLA-DPA10103-DPB10301" - "DRB1_0405" - "HLA-DQA10102-DQB10502" - "DRB3_0101" - "DRB1_1301" - "DRB1_0103" - "DRB1_0402" - "DRB1_0404" - "DRB1_0901" - "DRB3_0202" - "HLA-DQA10102-DQB10602" - "DRB5_0101" - "DRB5_0202" - "DRB1_0801" - "DRB4_0103" - "DRB1_0701" - "DRB1_1001" - "DRB1_0102" - "DRB1_0818" - "DRB1_1302" - "DRB1_0406" - "DRB1_0302" - "DRB1_1102" - "HLA-DPA10103-DPB10201" - "DRB1_1502" - "DRB1_1202" - "DRB4_0101" - "HLA-DQA10301-DQB10302" - "HLA-DPA10103-DPB10401" - "HLA-DQA10501-DQB10201" - "DRB1_0403" - "DRB1_0802" - "DRB1_1404" - "DRB1_1506" - "HLA-DQA10103-DQB10603" - "DRB1_1104" - "DRB3_0301" - "DRB1_0407" - "DRB1_1406" - "DRB1_1402" - "DRB1_1201" - "DRB1_1304" - "HLA-DPA10103-DPB10402" - "HLA-DQA10401-DQB10402" - "DRB1_1602" - "DRB1_1503" - "HLA-DQA10501-DQB10301" - "HLA-DQA10101-DQB10501" - "DRB1_0411" - "DRB1_1454" - "DRB5_0102" - "HLA-DPA10201-DPB11401" - "HLA-DQA10505-DQB10301" - "HLA-DQA10201-DQB10202" - "HLA-DPA10103-DPB10601" - "HLA-DQA10201-DQB10303" - "HLA-DPA10201-DPB10101" - "DRB1_0303" peptideLength: type: number description: "Length of peptide (all peptides of this length will be predicted, with max immunogenicity as final score)" default: 15 # Tmd Settings TmdSettings: type: object required: - proteinPDB - graphMode - ligandsSDF - nEqSteps - nFrames - stepsPerFrame - mpsWorkers properties: proteinPDB: type: string description: "Protein structure in PDB format File with extensions [pdb]" example: "1iep.pdb" format: binary graphMode: type: string description: "How ligands are connected in the perturbation network" default: "greedy" enum: - "greedy" - "star_map" - "custom" ligandsSDF: type: string description: "Ligands in SDF format (multiple molecules) File with extensions [sdf]" example: "tmd_example_ligands.sdf" format: binary alchemicalNetwork: type: string description: "Interactive preview and editor for the ligand perturbation network" networkEdges: type: string nEqSteps: type: number description: "Number of equilibration steps" minimum: 0 maximum: 1000000 default: 200000 nFrames: type: number description: "Number of production frames to generate" minimum: 10 maximum: 20000 default: 2000 stepsPerFrame: type: number description: "Number of MD steps per frame" minimum: 100 maximum: 5000 default: 400 mpsWorkers: type: number description: "Number of MPS processes per GPU for parallel edge execution" minimum: 1 maximum: 12 default: 1 # Tnp Settings TnpSettings: type: object required: - sequence properties: sequence: type: string description: "Sequence of your nanobody" example: "QVKLQESGAELARPGASVKLSCKASGYTFTNYWMQWVKQRPGQGLDWIGAIYPGDGNTRYTHKFKGKATLTADKSSSTAYMQLSSLASEDSGVYYCARGEGNYAWFAYWGQGTTVTVSS" # Unimol2 Settings Unimol2Settings: type: object required: - proteinFile - ligandFile - boxX - boxY - boxZ - width - height - depth properties: proteinFile: type: string example: "1iep.pdb" format: binary ligandFile: type: string description: "sdf structure file for your ligand (one ligand per file) File with extensions [sdf]" example: "Conformer3D_COMPOUND_CID_5291.sdf" format: binary boxX: type: number description: "X coordinate of bounding box center" example: "15.190" default: 35 boxY: type: number description: "Y coordinate of bounding box center" example: "53.903" default: 27 boxZ: type: number description: "Z coordinate of bounding box center" example: "16.917" default: 35 width: type: number description: "Width of bounding box" example: "20" default: 20 height: type: number description: "Height of bounding box" example: "20" default: 20 depth: type: number description: "Depth of bounding box" example: "20" default: 20 # Us-Align Settings UsAlignSettings: type: object required: - pdbFile1 - pdbFile2 properties: pdbFile1: type: string description: "Protein structure 1 in pdb format File with extensions [pdb]" example: "PDB1.pdb" format: binary pdbFile2: type: string description: "Protein structure 2 in pdb format File with extensions [pdb]" example: "PDB2.pdb" format: binary mm_opt: type: string default: "0: Two monomeric structures" enum: - "0: Two monomeric structures" - "1: Two multi-chain oligomeric structures" - "3: Circularly permuted structures" - "5: fNS alignment" - "6: sNS alignment" # Virtual-Screening Settings VirtualScreeningSettings: type: object required: - receptorFile - datasetId - dockingTool - boxX - boxY - boxZ - width - height - depth - exhaustiveness properties: receptorFile: type: string example: "1iep.pdb" format: binary datasetId: type: string description: "Select a ligand dataset to screen. Upload datasets at /ligands" example: "zinc-example" dockingTool: type: string example: "qvina02" default: "qvina02" enum: - "qvina02" boxX: type: number description: "X coordinate of bounding box center" example: "15.190" default: 0 boxY: type: number description: "Y coordinate of bounding box center" example: "53.903" default: 0 boxZ: type: number description: "Z coordinate of bounding box center" example: "16.917" default: 0 width: type: number description: "Width of bounding box" example: "20" default: 10 height: type: number description: "Height of bounding box" example: "20" default: 10 depth: type: number description: "Depth of bounding box" example: "20" default: 10 exhaustiveness: type: number description: "Adjusts the amount of computational effort used during a docking experiment - increasing this to 32 will give a more consistent docking result" example: "8" default: 8 # Zymctrl Settings ZymctrlSettings: type: object required: - fastaFile - ecNumber properties: fastaFile: type: string format: binary ecNumber: type: string description: "EC numbers describing your reaction of interest - find yours here: https://www.brenda-enzymes.org/ecexplorer.php?browser=1" example: "1.1.1.1" numSequences: type: number description: "Number of sequences to generate" default: 100 JobSubmission: type: object required: - jobName - type - settings properties: jobName: type: string description: Unique name for the job minLength: 1 maxLength: 100 pattern: '^[a-zA-Z0-9_-]+$' example: "my-protein-analysis" type: type: string description: Tool to use for the job example: "alphafold" # Tool enum ref enum: [abb4, abgpt, ablang, ablang-mpnn, abmap, abmpnn, abnativ, abodybuilder, adapt, admet, aev-plig, af-multistate, af-traj, af-unmasked, af2bind, af2rave, afcluster, afcycdesign, afsample, aggrescan3d, alde, align-pdbs, allmetal3d, alphabind-finetune, alphacutter, alphaflow, alphafold, amplify, anarci, ancestral-reconstruction, antiberty, antibody-annotation, antibody-diffusion-properties, antibody-evolution, antidif, antifold, apm, aqueous-solubility, atomsurf, autodock-vina, balm-finetune, balm-inference, balm-paired, bbmerge, bde, bindcraft, binding-ddg, bioemu, biophi, blast, boltz, boltz-finetune, boltzdesign, boltzgen, caliby, catpred, chai, charge-dipole, chembl, cluster-pdbs, colabdock, conformer-generation, contact-ms, cryfold, cryodrgn, custom-msa, dayhoff, deep-viscosity, deepfri, deepimmuno, deeprank-ab, deepsp, deepstabp, dfmdock, diffdock, diffsbdd, disco, dlkcat, dnaworks, dockq, drugflow, dsmbind, electronic-properties, electrostatic-potential, emboss, enumeration, enzygen2, enzygen2-finetune, enzygen2-inference, equidock, esm-embeddings, esm-if1, esm-scan, esm2, esmfold, evcouplings, evo2, evonb, evopro, evoprotgrad, fampnn, fastsolv, file-converter, fixbb, flowdock, foldmason, foldseek, fpocket, frameflow, frequency-analysis, fukui, g-mmpbsa, gbsa, gems, geometry-optimization, germinal, gnina, gromacs, gromacs-custom, hbond-strength, highfold, hmmalign, humatch, hypermpnn, idr, igblast, igdesign, iggm, immunebuilder, intercaat, intfold, ipc, ipsae, its-flexible, legolas, libinvent, lichen, ligandmpnn, logp, mage, masif, mavenets-finetune, mavenets-inference, mber, md-openmm, mdgen, membrane-gromacs, mhc-fine, microscopic-pka, min-distance-selected-residues, modelangelo, molecular-descriptors, molprobity, mosaic-hallucinate, mrnabert, msa, msa-analysis, msa-cluster, multi-evolve, n-linked-glycosylation, nampnn, nbforge, netmhcpan, netsolp, nos, nos-inference, oas, odesign-antibody, omegafold, openfe, openfold, openmm, openmm-metadynamics, openmm-relax, openmm-temperature-replica, orb-models, orb-models3, orthrus, paragraph, parasurf, pdbsum, pdockq, pepfunn, pepmlm, peppatch, peptiverse, pka, plabdab, placer, plm-finetune, plm-inference, pocketgen, ppap, ppiscreenml, process-atac, prodigy, profam, profluent-e1, progen2-finetune, progen2-inference, propka, prot-t5-embeddings, protein-design, protein-hunter, protein-metrics, protein-properties, protein-scoring, protein-sol, protein-solubilization, proteina-complexa, proteinmpnn, proteinmpnn-ddg, proteinmpnn-ddg-binder, proteinmpnn-score, protenix, proteus, protonation-state, psiblast, pubchem, pulchra, pxdesign, pykvfinder, pysca, qupkake, rbfe, reaction-energy, redox, reinvent-finetune, rf3, rfantibody, rfdiffusion, rfdiffusion-all-atom, rfdiffusion2, rfdiffusion3, rfpeptides, rhodesign, ribodiffusion, riffdiff, rmsd-calculator, rna-fm, rog, rosetta-ddg-prediction, rosetta-dock, rosetta-fixbb, rosetta-ppi, rosetta-relax, rosetta-relax-ligand, rosetta-score, roshambo, rso, saprot, saprot-finetune, search-conformations, single-point-energy, smina, space2, spatial-ppi, spin-state-energies, stabddg, structural-evolution, superwater, surfdock, syn-codon-lm, tap, tautomer, tcrmodel2, td-dft, tempro, temstapro, thermompnn, thermompnn-d, tlimmuno, tmd, tnp, unimol2, us-align, virtual-screening, zymctrl] settings: anyOf: # Tool settings ref - $ref: '#/components/schemas/Abb4Settings' - $ref: '#/components/schemas/AbgptSettings' - $ref: '#/components/schemas/AblangSettings' - $ref: '#/components/schemas/AblangMpnnSettings' - $ref: '#/components/schemas/AbmapSettings' - $ref: '#/components/schemas/AbmpnnSettings' - $ref: '#/components/schemas/AbnativSettings' - $ref: '#/components/schemas/AbodybuilderSettings' - $ref: '#/components/schemas/AdaptSettings' - $ref: '#/components/schemas/AdmetSettings' - $ref: '#/components/schemas/AevPligSettings' - $ref: '#/components/schemas/AfMultistateSettings' - $ref: '#/components/schemas/AfTrajSettings' - $ref: '#/components/schemas/AfUnmaskedSettings' - $ref: '#/components/schemas/Af2bindSettings' - $ref: '#/components/schemas/Af2raveSettings' - $ref: '#/components/schemas/AfclusterSettings' - $ref: '#/components/schemas/AfcycdesignSettings' - $ref: '#/components/schemas/AfsampleSettings' - $ref: '#/components/schemas/Aggrescan3dSettings' - $ref: '#/components/schemas/AldeSettings' - $ref: '#/components/schemas/AlignPdbsSettings' - $ref: '#/components/schemas/Allmetal3dSettings' - $ref: '#/components/schemas/AlphabindFinetuneSettings' - $ref: '#/components/schemas/AlphacutterSettings' - $ref: '#/components/schemas/AlphaflowSettings' - $ref: '#/components/schemas/AlphafoldSettings' - $ref: '#/components/schemas/AmplifySettings' - $ref: '#/components/schemas/AnarciSettings' - $ref: '#/components/schemas/AncestralReconstructionSettings' - $ref: '#/components/schemas/AntibertySettings' - $ref: '#/components/schemas/AntibodyAnnotationSettings' - $ref: '#/components/schemas/AntibodyDiffusionPropertiesSettings' - $ref: '#/components/schemas/AntibodyEvolutionSettings' - $ref: '#/components/schemas/AntidifSettings' - $ref: '#/components/schemas/AntifoldSettings' - $ref: '#/components/schemas/ApmSettings' - $ref: '#/components/schemas/AqueousSolubilitySettings' - $ref: '#/components/schemas/AtomsurfSettings' - $ref: '#/components/schemas/AutodockVinaSettings' - $ref: '#/components/schemas/BalmFinetuneSettings' - $ref: '#/components/schemas/BalmInferenceSettings' - $ref: '#/components/schemas/BalmPairedSettings' - $ref: '#/components/schemas/BbmergeSettings' - $ref: '#/components/schemas/BdeSettings' - $ref: '#/components/schemas/BindcraftSettings' - $ref: '#/components/schemas/BindingDdgSettings' - $ref: '#/components/schemas/BioemuSettings' - $ref: '#/components/schemas/BiophiSettings' - $ref: '#/components/schemas/BlastSettings' - $ref: '#/components/schemas/BoltzSettings' - $ref: '#/components/schemas/BoltzFinetuneSettings' - $ref: '#/components/schemas/BoltzdesignSettings' - $ref: '#/components/schemas/BoltzgenSettings' - $ref: '#/components/schemas/CalibySettings' - $ref: '#/components/schemas/CatpredSettings' - $ref: '#/components/schemas/ChaiSettings' - $ref: '#/components/schemas/ChargeDipoleSettings' - $ref: '#/components/schemas/ChemblSettings' - $ref: '#/components/schemas/ClusterPdbsSettings' - $ref: '#/components/schemas/ColabdockSettings' - $ref: '#/components/schemas/ConformerGenerationSettings' - $ref: '#/components/schemas/ContactMsSettings' - $ref: '#/components/schemas/CryfoldSettings' - $ref: '#/components/schemas/CryodrgnSettings' - $ref: '#/components/schemas/CustomMsaSettings' - $ref: '#/components/schemas/DayhoffSettings' - $ref: '#/components/schemas/DeepViscositySettings' - $ref: '#/components/schemas/DeepfriSettings' - $ref: '#/components/schemas/DeepimmunoSettings' - $ref: '#/components/schemas/DeeprankAbSettings' - $ref: '#/components/schemas/DeepspSettings' - $ref: '#/components/schemas/DeepstabpSettings' - $ref: '#/components/schemas/DfmdockSettings' - $ref: '#/components/schemas/DiffdockSettings' - $ref: '#/components/schemas/DiffsbddSettings' - $ref: '#/components/schemas/DiscoSettings' - $ref: '#/components/schemas/DlkcatSettings' - $ref: '#/components/schemas/DnaworksSettings' - $ref: '#/components/schemas/DockqSettings' - $ref: '#/components/schemas/DrugflowSettings' - $ref: '#/components/schemas/DsmbindSettings' - $ref: '#/components/schemas/ElectronicPropertiesSettings' - $ref: '#/components/schemas/ElectrostaticPotentialSettings' - $ref: '#/components/schemas/EmbossSettings' - $ref: '#/components/schemas/EnumerationSettings' - $ref: '#/components/schemas/Enzygen2Settings' - $ref: '#/components/schemas/Enzygen2FinetuneSettings' - $ref: '#/components/schemas/Enzygen2InferenceSettings' - $ref: '#/components/schemas/EquidockSettings' - $ref: '#/components/schemas/EsmEmbeddingsSettings' - $ref: '#/components/schemas/EsmIf1Settings' - $ref: '#/components/schemas/EsmScanSettings' - $ref: '#/components/schemas/Esm2Settings' - $ref: '#/components/schemas/EsmfoldSettings' - $ref: '#/components/schemas/EvcouplingsSettings' - $ref: '#/components/schemas/Evo2Settings' - $ref: '#/components/schemas/EvonbSettings' - $ref: '#/components/schemas/EvoproSettings' - $ref: '#/components/schemas/EvoprotgradSettings' - $ref: '#/components/schemas/FampnnSettings' - $ref: '#/components/schemas/FastsolvSettings' - $ref: '#/components/schemas/FileConverterSettings' - $ref: '#/components/schemas/FixbbSettings' - $ref: '#/components/schemas/FlowdockSettings' - $ref: '#/components/schemas/FoldmasonSettings' - $ref: '#/components/schemas/FoldseekSettings' - $ref: '#/components/schemas/FpocketSettings' - $ref: '#/components/schemas/FrameflowSettings' - $ref: '#/components/schemas/FrequencyAnalysisSettings' - $ref: '#/components/schemas/FukuiSettings' - $ref: '#/components/schemas/GMmpbsaSettings' - $ref: '#/components/schemas/GbsaSettings' - $ref: '#/components/schemas/GemsSettings' - $ref: '#/components/schemas/GeometryOptimizationSettings' - $ref: '#/components/schemas/GerminalSettings' - $ref: '#/components/schemas/GninaSettings' - $ref: '#/components/schemas/GromacsSettings' - $ref: '#/components/schemas/GromacsCustomSettings' - $ref: '#/components/schemas/HbondStrengthSettings' - $ref: '#/components/schemas/HighfoldSettings' - $ref: '#/components/schemas/HmmalignSettings' - $ref: '#/components/schemas/HumatchSettings' - $ref: '#/components/schemas/HypermpnnSettings' - $ref: '#/components/schemas/IdrSettings' - $ref: '#/components/schemas/IgblastSettings' - $ref: '#/components/schemas/IgdesignSettings' - $ref: '#/components/schemas/IggmSettings' - $ref: '#/components/schemas/ImmunebuilderSettings' - $ref: '#/components/schemas/IntercaatSettings' - $ref: '#/components/schemas/IntfoldSettings' - $ref: '#/components/schemas/IpcSettings' - $ref: '#/components/schemas/IpsaeSettings' - $ref: '#/components/schemas/ItsFlexibleSettings' - $ref: '#/components/schemas/LegolasSettings' - $ref: '#/components/schemas/LibinventSettings' - $ref: '#/components/schemas/LichenSettings' - $ref: '#/components/schemas/LigandmpnnSettings' - $ref: '#/components/schemas/LogpSettings' - $ref: '#/components/schemas/MageSettings' - $ref: '#/components/schemas/MasifSettings' - $ref: '#/components/schemas/MavenetsFinetuneSettings' - $ref: '#/components/schemas/MavenetsInferenceSettings' - $ref: '#/components/schemas/MberSettings' - $ref: '#/components/schemas/MdOpenmmSettings' - $ref: '#/components/schemas/MdgenSettings' - $ref: '#/components/schemas/MembraneGromacsSettings' - $ref: '#/components/schemas/MhcFineSettings' - $ref: '#/components/schemas/MicroscopicPkaSettings' - $ref: '#/components/schemas/MinDistanceSelectedResiduesSettings' - $ref: '#/components/schemas/ModelangeloSettings' - $ref: '#/components/schemas/MolecularDescriptorsSettings' - $ref: '#/components/schemas/MolprobitySettings' - $ref: '#/components/schemas/MosaicHallucinateSettings' - $ref: '#/components/schemas/MrnabertSettings' - $ref: '#/components/schemas/MsaSettings' - $ref: '#/components/schemas/MsaAnalysisSettings' - $ref: '#/components/schemas/MsaClusterSettings' - $ref: '#/components/schemas/MultiEvolveSettings' - $ref: '#/components/schemas/NLinkedGlycosylationSettings' - $ref: '#/components/schemas/NampnnSettings' - $ref: '#/components/schemas/NbforgeSettings' - $ref: '#/components/schemas/NetmhcpanSettings' - $ref: '#/components/schemas/NetsolpSettings' - $ref: '#/components/schemas/NosSettings' - $ref: '#/components/schemas/NosInferenceSettings' - $ref: '#/components/schemas/OasSettings' - $ref: '#/components/schemas/OdesignAntibodySettings' - $ref: '#/components/schemas/OmegafoldSettings' - $ref: '#/components/schemas/OpenfeSettings' - $ref: '#/components/schemas/OpenfoldSettings' - $ref: '#/components/schemas/OpenmmSettings' - $ref: '#/components/schemas/OpenmmMetadynamicsSettings' - $ref: '#/components/schemas/OpenmmRelaxSettings' - $ref: '#/components/schemas/OpenmmTemperatureReplicaSettings' - $ref: '#/components/schemas/OrbModelsSettings' - $ref: '#/components/schemas/OrbModels3Settings' - $ref: '#/components/schemas/OrthrusSettings' - $ref: '#/components/schemas/ParagraphSettings' - $ref: '#/components/schemas/ParasurfSettings' - $ref: '#/components/schemas/PdbsumSettings' - $ref: '#/components/schemas/PdockqSettings' - $ref: '#/components/schemas/PepfunnSettings' - $ref: '#/components/schemas/PepmlmSettings' - $ref: '#/components/schemas/PeppatchSettings' - $ref: '#/components/schemas/PeptiverseSettings' - $ref: '#/components/schemas/PkaSettings' - $ref: '#/components/schemas/PlabdabSettings' - $ref: '#/components/schemas/PlacerSettings' - $ref: '#/components/schemas/PlmFinetuneSettings' - $ref: '#/components/schemas/PlmInferenceSettings' - $ref: '#/components/schemas/PocketgenSettings' - $ref: '#/components/schemas/PpapSettings' - $ref: '#/components/schemas/PpiscreenmlSettings' - $ref: '#/components/schemas/ProcessAtacSettings' - $ref: '#/components/schemas/ProdigySettings' - $ref: '#/components/schemas/ProfamSettings' - $ref: '#/components/schemas/ProfluentE1Settings' - $ref: '#/components/schemas/Progen2FinetuneSettings' - $ref: '#/components/schemas/Progen2InferenceSettings' - $ref: '#/components/schemas/PropkaSettings' - $ref: '#/components/schemas/ProtT5EmbeddingsSettings' - $ref: '#/components/schemas/ProteinDesignSettings' - $ref: '#/components/schemas/ProteinHunterSettings' - $ref: '#/components/schemas/ProteinMetricsSettings' - $ref: '#/components/schemas/ProteinPropertiesSettings' - $ref: '#/components/schemas/ProteinScoringSettings' - $ref: '#/components/schemas/ProteinSolSettings' - $ref: '#/components/schemas/ProteinSolubilizationSettings' - $ref: '#/components/schemas/ProteinaComplexaSettings' - $ref: '#/components/schemas/ProteinmpnnSettings' - $ref: '#/components/schemas/ProteinmpnnDdgSettings' - $ref: '#/components/schemas/ProteinmpnnDdgBinderSettings' - $ref: '#/components/schemas/ProteinmpnnScoreSettings' - $ref: '#/components/schemas/ProtenixSettings' - $ref: '#/components/schemas/ProteusSettings' - $ref: '#/components/schemas/ProtonationStateSettings' - $ref: '#/components/schemas/PsiblastSettings' - $ref: '#/components/schemas/PubchemSettings' - $ref: '#/components/schemas/PulchraSettings' - $ref: '#/components/schemas/PxdesignSettings' - $ref: '#/components/schemas/PykvfinderSettings' - $ref: '#/components/schemas/PyscaSettings' - $ref: '#/components/schemas/QupkakeSettings' - $ref: '#/components/schemas/RbfeSettings' - $ref: '#/components/schemas/ReactionEnergySettings' - $ref: '#/components/schemas/RedoxSettings' - $ref: '#/components/schemas/ReinventFinetuneSettings' - $ref: '#/components/schemas/Rf3Settings' - $ref: '#/components/schemas/RfantibodySettings' - $ref: '#/components/schemas/RfdiffusionSettings' - $ref: '#/components/schemas/RfdiffusionAllAtomSettings' - $ref: '#/components/schemas/Rfdiffusion2Settings' - $ref: '#/components/schemas/Rfdiffusion3Settings' - $ref: '#/components/schemas/RfpeptidesSettings' - $ref: '#/components/schemas/RhodesignSettings' - $ref: '#/components/schemas/RibodiffusionSettings' - $ref: '#/components/schemas/RiffdiffSettings' - $ref: '#/components/schemas/RmsdCalculatorSettings' - $ref: '#/components/schemas/RnaFmSettings' - $ref: '#/components/schemas/RogSettings' - $ref: '#/components/schemas/RosettaDdgPredictionSettings' - $ref: '#/components/schemas/RosettaDockSettings' - $ref: '#/components/schemas/RosettaFixbbSettings' - $ref: '#/components/schemas/RosettaPpiSettings' - $ref: '#/components/schemas/RosettaRelaxSettings' - $ref: '#/components/schemas/RosettaRelaxLigandSettings' - $ref: '#/components/schemas/RosettaScoreSettings' - $ref: '#/components/schemas/RoshamboSettings' - $ref: '#/components/schemas/RsoSettings' - $ref: '#/components/schemas/SaprotSettings' - $ref: '#/components/schemas/SaprotFinetuneSettings' - $ref: '#/components/schemas/SearchConformationsSettings' - $ref: '#/components/schemas/SinglePointEnergySettings' - $ref: '#/components/schemas/SminaSettings' - $ref: '#/components/schemas/Space2Settings' - $ref: '#/components/schemas/SpatialPpiSettings' - $ref: '#/components/schemas/SpinStateEnergiesSettings' - $ref: '#/components/schemas/StabddgSettings' - $ref: '#/components/schemas/StructuralEvolutionSettings' - $ref: '#/components/schemas/SuperwaterSettings' - $ref: '#/components/schemas/SurfdockSettings' - $ref: '#/components/schemas/SynCodonLmSettings' - $ref: '#/components/schemas/TapSettings' - $ref: '#/components/schemas/TautomerSettings' - $ref: '#/components/schemas/Tcrmodel2Settings' - $ref: '#/components/schemas/TdDftSettings' - $ref: '#/components/schemas/TemproSettings' - $ref: '#/components/schemas/TemstaproSettings' - $ref: '#/components/schemas/ThermompnnSettings' - $ref: '#/components/schemas/ThermompnnDSettings' - $ref: '#/components/schemas/TlimmunoSettings' - $ref: '#/components/schemas/TmdSettings' - $ref: '#/components/schemas/TnpSettings' - $ref: '#/components/schemas/Unimol2Settings' - $ref: '#/components/schemas/UsAlignSettings' - $ref: '#/components/schemas/VirtualScreeningSettings' - $ref: '#/components/schemas/ZymctrlSettings' description: Tool-specific settings additionalProperties: true BatchSubmission: type: object required: - batchName - type - settings - jobNames properties: batchName: type: string description: Unique name for the batch minLength: 1 maxLength: 100 pattern: '^[a-zA-Z0-9_-]+$' example: "my-batch-analysis" type: type: string description: Tool to use for the batch example: "alphafold" # Tool enum ref enum: [abb4, abgpt, ablang, ablang-mpnn, abmap, abmpnn, abnativ, abodybuilder, adapt, admet, aev-plig, af-multistate, af-traj, af-unmasked, af2bind, af2rave, afcluster, afcycdesign, afsample, aggrescan3d, alde, align-pdbs, allmetal3d, alphabind-finetune, alphacutter, alphaflow, alphafold, amplify, anarci, ancestral-reconstruction, antiberty, antibody-annotation, antibody-diffusion-properties, antibody-evolution, antidif, antifold, apm, aqueous-solubility, atomsurf, autodock-vina, balm-finetune, balm-inference, balm-paired, bbmerge, bde, bindcraft, binding-ddg, bioemu, biophi, blast, boltz, boltz-finetune, boltzdesign, boltzgen, caliby, catpred, chai, charge-dipole, chembl, cluster-pdbs, colabdock, conformer-generation, contact-ms, cryfold, cryodrgn, custom-msa, dayhoff, deep-viscosity, deepfri, deepimmuno, deeprank-ab, deepsp, deepstabp, dfmdock, diffdock, diffsbdd, disco, dlkcat, dnaworks, dockq, drugflow, dsmbind, electronic-properties, electrostatic-potential, emboss, enumeration, enzygen2, enzygen2-finetune, enzygen2-inference, equidock, esm-embeddings, esm-if1, esm-scan, esm2, esmfold, evcouplings, evo2, evonb, evopro, evoprotgrad, fampnn, fastsolv, file-converter, fixbb, flowdock, foldmason, foldseek, fpocket, frameflow, frequency-analysis, fukui, g-mmpbsa, gbsa, gems, geometry-optimization, germinal, gnina, gromacs, gromacs-custom, hbond-strength, highfold, hmmalign, humatch, hypermpnn, idr, igblast, igdesign, iggm, immunebuilder, intercaat, intfold, ipc, ipsae, its-flexible, legolas, libinvent, lichen, ligandmpnn, logp, mage, masif, mavenets-finetune, mavenets-inference, mber, md-openmm, mdgen, membrane-gromacs, mhc-fine, microscopic-pka, min-distance-selected-residues, modelangelo, molecular-descriptors, molprobity, mosaic-hallucinate, mrnabert, msa, msa-analysis, msa-cluster, multi-evolve, n-linked-glycosylation, nampnn, nbforge, netmhcpan, netsolp, nos, nos-inference, oas, odesign-antibody, omegafold, openfe, openfold, openmm, openmm-metadynamics, openmm-relax, openmm-temperature-replica, orb-models, orb-models3, orthrus, paragraph, parasurf, pdbsum, pdockq, pepfunn, pepmlm, peppatch, peptiverse, pka, plabdab, placer, plm-finetune, plm-inference, pocketgen, ppap, ppiscreenml, process-atac, prodigy, profam, profluent-e1, progen2-finetune, progen2-inference, propka, prot-t5-embeddings, protein-design, protein-hunter, protein-metrics, protein-properties, protein-scoring, protein-sol, protein-solubilization, proteina-complexa, proteinmpnn, proteinmpnn-ddg, proteinmpnn-ddg-binder, proteinmpnn-score, protenix, proteus, protonation-state, psiblast, pubchem, pulchra, pxdesign, pykvfinder, pysca, qupkake, rbfe, reaction-energy, redox, reinvent-finetune, rf3, rfantibody, rfdiffusion, rfdiffusion-all-atom, rfdiffusion2, rfdiffusion3, rfpeptides, rhodesign, ribodiffusion, riffdiff, rmsd-calculator, rna-fm, rog, rosetta-ddg-prediction, rosetta-dock, rosetta-fixbb, rosetta-ppi, rosetta-relax, rosetta-relax-ligand, rosetta-score, roshambo, rso, saprot, saprot-finetune, search-conformations, single-point-energy, smina, space2, spatial-ppi, spin-state-energies, stabddg, structural-evolution, superwater, surfdock, syn-codon-lm, tap, tautomer, tcrmodel2, td-dft, tempro, temstapro, thermompnn, thermompnn-d, tlimmuno, tmd, tnp, unimol2, us-align, virtual-screening, zymctrl] settings: type: array description: List of job settings to submit minItems: 1 maxItems: 100 items: $ref: '#/components/schemas/JobSubmission/properties/settings' jobNames: type: array description: List of job names to submit corresponding to the job settings minItems: 1 maxItems: 100 items: $ref: '#/components/schemas/JobSubmission/properties/jobName' JobResponse: type: object properties: message: type: string description: Response message example: "Job submitted successfully" BatchResponse: type: object properties: batchName: type: string description: Name of the submitted batch jobs: type: array items: $ref: '#/components/schemas/JobResponse' totalJobs: type: integer description: Total number of jobs in the batch JobInfo: type: object properties: JobName: type: string description: Name of the job Type: type: string description: Tool used for the job JobStatus: type: string enum: ["Complete", "In Queue", "Running", "Stopped", "Deleted"] description: Current status of the job Created: type: string format: date-time description: When the job was created Started: type: string format: date-time description: When the job started (if applicable) Completed: type: string format: date-time description: When the job completed (if applicable) Settings: type: object description: Job settings and parameters (stored as JSON string) additionalProperties: true Score: type: number description: Job score (if applicable) Batch: type: boolean description: Whether this is a batch job User: type: string description: User who created the job (only present in organization queries) JobResult: type: object properties: jobName: type: string description: Name of the job status: type: string enum: [pending, running, completed, failed, cancelled] description: Current status of the job results: type: object description: Job results (structure varies by tool) additionalProperties: true error: type: string description: Error message if job failed outputFiles: type: array description: List of output files items: type: object properties: fileName: type: string description: Name of the output file fileUrl: type: string description: URL to download the file fileType: type: string description: Type of the file (PDB, JSON, etc.) ErrorResponse: type: object properties: error: type: string description: Error message code: type: string description: Error code details: type: object description: Additional error details tags: - name: Jobs description: Job submission and management - name: Files description: File upload and management - name: Results description: Job results retrieval