AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
1
Cyclic
Optional settings
Use YAML file input
Upload a Boltz YAML configuration file instead of filling out the UI. MSA entries are not required — MSAs are computed and injected automatically for protein chains.
Number of Recycles
Number of rounds of refinement during structure prediction. Higher values may improve accuracy but take longer.
Step Scale
Lower step scale means more diversity (recommended between 1 and 2).
Number of Seeds
Number of jobs to submit. Each job uses a random seed by default.
Seed (optional)
Set a specific seed for reproducibility, or leave blank for a random seed.
Output Format
File format used for predicted structures.
Boltz Version
Which Boltz model version to use for prediction.
Method
Experimental method bias for the prediction (optional).
Template CIFs
Upload template CIF files to guide the structure prediction. These will be used as templates for the prediction.
Template Distance Threshold
Controls the distance (in Angstroms) that the prediction can deviate from the template.
Use Potentials
Run the original Boltz-2 model using inference time potentials. Significantly improves the physical quality of the poses.
Use Multiple Sequence Alignment
When disabled, Boltz will not use MSA data for prediction.
Custom A3M Files
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. MSA generation is skipped for chains you provide an a3m for.
Max MSA Sequences
Max number of sequences to use for MSA. Use a smaller value for a more shallow MSA, which may produce predictions closer to your template.
MSA Database
Sequence database to search when building the MSA. UniRef30 searches are extended with the ColabFold environmental database (BFD/MGnify-derived). SwissProt restricts the search to curated SwissProt sequences.
Generate IPSAE metrics
Generate IPSAE metrics for protein-protein complex interfaces.
All sequences must be non empty.
Structure Prediction