SwissDock Dock Ligand

Overview

Perform protein-ligand molecular docking using SwissDock service with AutoDock Vina or Attracting Cavities 2.0 engines. Predicts binding modes, poses, and energies for small molecules against protein structures. Essential for drug discovery, virtual screening, and structure-based drug design. Supports blind docking (whole protein) or targeted docking (specific binding site). Returns docking scores, poses, and download URL for detailed results. Example: Dock aspirin (CC(=O)Oc1ccccc1C(=O)O) against COX-2 (PDB: 1CX2) to predict binding mode and affinity.

Status

Succeeds, but routinely takes more than 8 seconds. Hidden from the agent's default toolset; available via opt-in.

Note: Async docking job; returns a session_id polled via SwissDock_check_job_status / SwissDock_retrieve_results.

Last probed

never

Last success

never

Last latency

—

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "box_center": {
      "default": null,
      "description": "Binding site center coordinates as 'x,y,z' in Angstroms. If not provided, performs blind docking (whole protein). Example: '10.5,20.3,15.8'",
      "type": "string"
    },
    "box_size": {
      "default": null,
      "description": "Search box dimensions as 'a,b,c' in Angstroms. If not provided, uses default size. Example: '20,20,20' for 20x20x20 Angstrom box.",
      "type": "string"
    },
    "docking_engine": {
      "default": "attracting_cavities",
      "description": "Docking engine: 'attracting_cavities' (cavity-based, default, recommended for blind docking) or 'vina' (AutoDock Vina, faster for targeted docking). Example: Use 'attracting_cavities' for whole-protein screening, 'vina' for known binding site.",
      "enum": [
        "attracting_cavities",
        "vina"
      ],
      "type": "string"
    },
    "exhaustiveness": {
      "default": 8,
      "description": "Search exhaustiveness (1-20). Higher values increase accuracy but take longer. Default: 8. Use 16-20 for publication-quality results. Example: Use 8 for quick screening, 16 for final validation.",
      "type": "integer"
    },
    "ligand_smiles": {
      "description": "SMILES string of the ligand/small molecule to dock. Example: 'CC(=O)Oc1ccccc1C(=O)O' for aspirin",
      "type": "string"
    },
    "pdb_id": {
      "description": "4-character PDB ID of the target protein structure. Example: '1ATP' for protein kinase A",
      "type": "string"
    }
  },
  "required": [
    "ligand_smiles",
    "pdb_id"
  ],
  "type": "object"
}

Examples (1)

{
  "exhaustiveness": 1,
  "ligand_smiles": "",
  "pdb_id": "1AKI"
}

Identifiers

Catalog ID

tu_SwissDock_dock_ligand

Tool name

SwissDock_dock_ligand

Added

2026-04-30 22:47Z

Tags

tooluniverse, slow