- All Tools
- Database
- Batch Workflows
- Pipelines
- Contact
- Blog
- Docs
- API
- Pricing
API Documentation
Overview
API Key
/tools
/submit-job
/submit-batch
/jobs
/result
/delete-job
/upload/{filename}
/files
/delete-file
/run-pipeline
/submit-pipeline
Submit Single Jobs
The POST API endpoint /submit-job allows users to submit jobs to Tamarind. These jobs are visible in the same queue as jobs submitted through the UI. You may choose your job type and settings below to configure your job.
Options for inputting file fields (ex. .pdb, .sdf, etc.):
- Use the /upload endpoint and upload your file before submitting
- Use the path of a previous Tamarind job, in the format JobName/path/to/file.ext
- Submit the contents of your file directly
Select tool:
Settings
Protein amino acid sequence, use : to separate chains for multimers
Options: ["1", "2", "3", "4", "5"]
Default: 5
Number of Models: Number of models to be used, each generating a different prediction
Options: ["mmseqs2_uniref_env", "mmseqs2_uniref", "single_sequence"]
MSA Mode: Select which database to use for MSA, or choose 'single_sequence' to skip MSA search
Default: 3
Number of recycles: Number of times to recycle outputs back through structure prediction process for refined results
Default: 0
Number of models to relax: Number of models to perform amber relaxation for more accurate side chain predictions
Options: ["paired", "unpaired", "unpaired_paired"]
Pair Mode: "unpaired_paired" = pair sequences from same species + unpaired MSA, "unpaired" = seperate MSA for each chain, "paired" - only use paired sequences.
Default: True
Use PDB 100 Templates: Query PDB100 for template structures to use for your prediction
Custom Template Files: Use custom structural templates in your prediction
Random seed: Random seed to be used in structure prediction
Options: ["508:2048", "512:1024", "256:512", "128:256", "64:128", "32:64", "16:32"]
Max MSA: Max # Clusters : Max # Extra Sequences - decrease max_msa to increase uncertainity
Options: ["0.0", "0.5", "1.0"]
Recycle Early Stop Tolerance: Run recycles until distance between recycles is within a given tolerance (0 = never stop early)
Default: False
Score with IPSAE: Use IPSAE scoring function for interprotein interactions
Default: False
1import requests
2
3api_key = "***************"
4headers = {'x-api-key': api_key}
5base_url = "https://app.tamarind.bio/api/"
6
7params = {
8 "jobName": "myJobName",
9 "type": "alphafold",
10 "settings": {
11 "sequence": "MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV"
12 }
13}
14response = requests.post(base_url + "submit-job", headers=headers, json=params)
15print(response.text)Chat
Welcome to Tamarind Bio! Ask me anything about the Tamarind platform and available tools.