submit_docking_workflow
Submit molecular docking workflows to predict ligand binding in proteins using PDB IDs, SMILES strings, and binding pocket coordinates with configurable software and scoring options.
Instructions
Submits a Docking workflow to the API.
Args: protein: Protein for docking. Can be: 1) PDB ID string (e.g., '1HCK'), 2) Protein UUID string, 3) JSON string dict with 'pdb_id' and optional 'name' pocket: Binding pocket as JSON string "[[x1,y1,z1], [x2,y2,z2]]" defining two opposite corners of the docking box initial_molecule: SMILES string representing the ligand executable: Docking software (default: 'vina'). Options: 'vina', 'qvina2', 'smina' scoring_function: Scoring function (default: 'vinardo'). Options: 'vina', 'vinardo', 'ad4' exhaustiveness: Search exhaustiveness (default: 8). Higher values = more thorough but slower do_csearch: Whether to perform conformational search on the ligand before docking (default: False) do_optimization: Whether to optimize the ligand geometry before docking (default: False) do_pose_refinement: Whether to optimize non-rotatable bonds in output poses (default: False) name: Workflow name for identification and tracking folder_uuid: UUID of folder to organize this workflow. Empty string uses default folder. max_credits: Maximum credits to spend on this calculation. 0 for no limit.
Automatically handles protein creation from PDB ID and sanitization if needed.
Returns: Workflow object representing the submitted workflow
Examples: # Example 1: Using PDB ID directly result = submit_docking_workflow( protein="1HCK", # PDB ID pocket="[[103.55, 100.59, 82.99], [27.76, 32.67, 48.79]]", initial_molecule="CCC(C)(C)NC1=NCC2(CCC(=O)C2C)N1", name="CDK2 Docking" )
# Example 2: Using dict with PDB ID and custom name
result = submit_docking_workflow(
protein='{"pdb_id": "1HCK", "name": "My CDK2 Protein"}',
pocket="[[103.55, 100.59, 82.99], [27.76, 32.67, 48.79]]",
initial_molecule="CCC(C)(C)NC1=NCC2(CCC(=O)C2C)N1"
)
# Example 3: Using existing protein UUID
result = submit_docking_workflow(
protein="abc123-def456-...", # Protein UUID
pocket="[[103.55, 100.59, 82.99], [27.76, 32.67, 48.79]]",
initial_molecule="CCC(C)(C)NC1=NCC2(CCC(=O)C2C)N1"
)Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| protein | Yes | Protein UUID or PDB content/path for docking target | |
| Yes | JSON string defining binding pocket as [[x1,y1,z1], [x2,y2,z2]] corner coordinates | ||
| initial_molecule | Yes | SMILES string of the ligand molecule to dock | |
| executable | No | Docking software to use: 'vina', 'qvina2', 'smina' | vina |
| scoring_function | No | Scoring function: 'vina', 'vinardo', 'ad4' | vinardo |
| exhaustiveness | No | Search exhaustiveness parameter (higher = more thorough, slower) | |
| do_csearch | No | Whether to perform conformer search before docking | |
| do_optimization | No | Whether to optimize docked poses | |
| do_pose_refinement | No | Whether to optimize output poses with non-rotatable bond refinement | |
| name | No | Workflow name for identification and tracking | Docking Workflow |
| 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 |