Equidock¶
Runs protein–protein docking of one or more ligand structures against a single receptor using the EquiDock model. It returns the ligand structure(s) transformed into the receptor’s coordinate frame, with an option to post-process to reduce steric clashes.
Usage¶
Use this node when you need to dock protein ligand(s) to a receptor structure. Typical workflow: load or prepare ligand PDB(s) and a single receptor PDB, select the EquiDock checkpoint variant (dataset), optionally enable clash removal, then route the docked ligand output to downstream analysis or save steps.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| ligand_pdb | True | PDB | One or multiple ligand structure files in PDB format to be docked. Provide as a mapping of names to PDB contents. | {'ligand_A.pdb': 'ATOM ...', 'ligand_B.pdb': 'ATOM ...'} |
| receptor_pdb | True | PDB | Single receptor structure in PDB format to dock against. Only one receptor is supported. | {'receptor.pdb': 'ATOM ...'} |
| dataset | True | dips \| db5 | Selects which EquiDock training checkpoint to use, corresponding to the dataset variant. Use the one matching your expected domain. | dips |
| remove_clashes | True | BOOLEAN | If true, applies a post-processing step to reduce steric clashes in the docked ligands. | False |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| bound_ligand.pdb | PDB | Docked ligand structure(s) in PDB format, aligned to the receptor frame. If multiple ligands were provided, returns a mapping of names to docked PDB contents. | {'ligand_A_docked.pdb': 'ATOM ...', 'ligand_B_docked.pdb': 'ATOM ...'} |
Important Notes¶
- Single receptor only: The node rejects inputs with more than one receptor PDB.
- Multiple ligands supported: You can dock several ligands in one run; all will be aligned to the provided receptor.
- Checkpoint selection: The 'dataset' choice (dips or db5) determines which EquiDock checkpoint is used and can impact docking behavior.
- Clash removal: Enabling 'remove_clashes' may slightly adjust coordinates to resolve steric conflicts.
Troubleshooting¶
- Error: multiple receptors provided: Provide exactly one receptor PDB; split multiple receptors into separate runs.
- Invalid PDB input: Ensure PDB strings are well-formed and non-empty; malformed PDB content may cause failures.
- Unexpected docking quality: Try changing the 'dataset' option (dips vs db5) or enabling 'remove_clashes' to improve results.
- Output missing for some ligands: Verify each ligand PDB is valid; remove problematic ligands and retry to isolate issues.