submit_protein_cofolding_workflow
Submit protein-ligand cofolding workflows to predict 3D structures and calculate binding affinity using computational chemistry models.
Instructions
Submits a protein cofolding workflow to the API.
Args: initial_protein_sequences: JSON string list of protein sequences (amino acid strings) to cofold initial_smiles_list: JSON string list of ligand SMILES strings to include in cofolding. None for protein-only ligand_binding_affinity_index: Index of ligand in initial_smiles_list for binding affinity calculation (e.g., "0"). None skips affinity use_msa_server: Whether to use MSA (Multiple Sequence Alignment) server for improved accuracy use_potentials: Whether to use statistical potentials in the calculation compute_strain: Whether to compute the strain of the pose (if pose_refinement is enabled) do_pose_refinement: Whether to optimize non-rotatable bonds in output poses name: Workflow name for identification and tracking model: Cofolding model to use (defaults to stjames.CofoldingModel.BOLTZ_2.value) folder_uuid: UUID of folder to organize this workflow. None uses default folder. max_credits: Maximum credits to spend on this calculation. None for no limit.
Returns: Workflow object representing the submitted workflow
Example: # Torcetrapib Cofolding result = submit_protein_cofolding_workflow( initial_protein_sequences='["ASKGTSHEAGIVCRITKPALLVLNHETAKVIQTAFQRASYPDITGEKAMMLLGQVKYGLHNIQISHLSIASSQVELVEAKSIDVSIQDVSVVFKGTLKYGYTTAWWLGIDQSIDFEIDSAIDLQINTQLTADSGRVRTDAPDCYLSFHKLLLHLQGEREPGWIKQLFTNFISFTLKLVLKGQICKEINVISNIMADFVQTRAASILSDGDIGVDISLTGDPVITASYLESHHKGHFIYKDVSEDLPLPTFSPTLLGDSRMLYFWFSERVFHSLAKVAFQDGRLMLSLMGDEFKAVLETWGFNTNQEIFQEVVGGFPSQAQVTVHCLKMPKISCQNKGVVVDSSVMVKFLFPRPDQQHSVAYTFEEDIVTTVQASYSKKKLFLSLLDFQITPKTVSNLTESSSESIQSFLQSMITAVGIPEVMSRLEVVFTALMNSKGVSLFDIINPEIITRDGFLLLQMDFGFPEHLLVDFLQSLS"]', initial_smiles_list='["CCOC(=O)N1c2ccc(C(F)(F)F)cc2C@@HC[C@H]1CC"]', ligand_binding_affinity_index="0", name="Torcetrapib Cofolding", do_pose_refinement=True, compute_strain=True )
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| initial_protein_sequences | Yes | JSON string list of protein sequences for cofolding (e.g., '["MKLLV...", "MAHQR..."]') | |
| initial_smiles_list | No | JSON string list of SMILES for ligands to include in cofolding (e.g., '["CCO", "CC(=O)O"]'). Empty for protein-only | |
| ligand_binding_affinity_index | No | Index of ligand for binding affinity computation (e.g., '0'). Empty for no affinity calculation | |
| use_msa_server | No | Whether to use multiple sequence alignment server for better structure prediction | |
| use_potentials | No | Whether to include additional potentials in the calculation | |
| compute_strain | No | Whether to compute the strain of the pose (if pose_refinement is enabled) | |
| do_pose_refinement | No | Whether to optimize non-rotatable bonds in output poses | |
| name | No | Workflow name for identification and tracking | Cofolding Workflow |
| model | No | Structure prediction model to use (e.g., 'boltz_2', 'alphafold3') | boltz_2 |
| folder_uuid | No | UUID of folder to organize this workflow. Empty string uses default folder | |
| max_credits | No | Maximum credits to spend on this calculation. 0 for no limit |