Equidock¶
Runs protein–protein docking using the EquiDock model. It docks one or more ligand structures into a single receptor structure and returns the ligand(s) transformed into the receptor frame. Optionally performs post-processing to reduce steric clashes.
Usage¶
Use this node when you need to predict how a ligand protein binds to a receptor protein. Typical workflow: load ligand PDB(s) and a single receptor PDB with a loader node, choose the EquiDock training dataset variant (dips or db5) that matches your use case, optionally enable clash removal, then connect the output to downstream analysis or save steps.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| ligand_pdb | True | PDB | Ligand structure(s) to dock. Supports one or multiple ligands. Usually provided by a Load PDB node as a mapping from filenames/IDs to PDB text. | {'ligand1.pdb': 'ATOM ...', 'ligand2.pdb': 'ATOM ...'} |
| receptor_pdb | True | PDB | Receptor structure to dock against. Must contain exactly one receptor entry. | {'receptor.pdb': 'ATOM ...'} |
| dataset | True | CHOICE | EquiDock checkpoint variant used for inference. Select the dataset the model was trained on. | dips |
| remove_clashes | True | BOOLEAN | If true, post-processes docked ligands to mitigate steric clashes. | False |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| bound_ligand.pdb | PDB | Docked ligand structure(s) transformed into the receptor coordinate frame. If multiple ligands were provided, returns all corresponding docked ligands. | {'ligand1_docked.pdb': 'ATOM ...', 'ligand2_docked.pdb': 'ATOM ...'} |
Important Notes¶
- Single receptor only: The node does not support multiple receptors; provide exactly one receptor PDB entry.
- Multiple ligands supported: You may input more than one ligand; outputs will include all docked ligands.
- Dataset choice: Selecting the appropriate dataset variant (dips or db5) can affect performance; use the one aligned with your target domain.
- Input format: PDB inputs are expected as a mapping from a name (e.g., filename) to PDB text, typically sourced from a PDB loader node.
Troubleshooting¶
- Error: multiple receptors provided: Ensure the receptor_pdb input contains exactly one entry. Split receptors into separate runs if needed.
- Empty or failed docking result: Verify that the input PDB files are valid and properly formatted; remove non-standard residues or alternate locations if necessary.
- Unexpected geometry after clash removal: Disable remove_clashes to check the raw docking result; then adjust preprocessing or try the alternative dataset setting.
- Output naming confusion: If multiple ligands were input, check output keys (e.g., ligand1_docked.pdb, ligand2_docked.pdb) to map each result to its corresponding input.