ProteinsPlus Predict Binding Sites V3

Overview

Predict druggable binding sites using DoGSite3 algorithm with ligand-biased grid option. Enhanced version of DoGSiteScorer with improved binding site detection. Input can be a PDB ID with optional reference ligand for biased grid calculations. Returns predicted pockets with druggability scores, geometric properties, and detailed subpocket analysis. Supports ligand-based grid biasing to focus predictions around known binding sites. Useful for comprehensive binding site characterization and structure-based drug design workflows. Example: Analyze 1KZK with ligand JE2_A_701 to identify druggable sites near the co-crystallized ligand.

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed

1d ago

Last success

1d ago

Last latency

110ms

Schema

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

{
  "properties": {
    "analysis_detail": {
      "description": "Analysis level: '0' for pockets only (faster), '1' for pockets and subpockets (comprehensive). Default: '1'. Example: Use '1' for detailed analysis, '0' for quick screening.",
      "enum": [
        "0",
        "1"
      ],
      "type": "string"
    },
    "chain": {
      "description": "Specific chain to analyze (e.g., 'A'). Optional - if not provided, all chains analyzed.",
      "type": "string"
    },
    "druggability": {
      "description": "Prediction granularity: '0' for geometric properties only, '1' for properties and druggability scores. Default: '1'. Example: Use '1' for drug discovery (includes druggability), '0' for structure analysis only.",
      "enum": [
        "0",
        "1"
      ],
      "type": "string"
    },
    "ligand": {
      "description": "Reference ligand identifier in format 'residue_name_residue_chain_residue_number' (e.g., 'JE2_A_701'). Optional - used for ligand-biased grid calculations.",
      "type": "string"
    },
    "ligand_bias": {
      "description": "Enable ligand-biased grid calculations (true) or standard detection (false). Requires ligand parameter. Default: false. Example: Use true to focus detection around known binding site.",
      "type": "boolean"
    },
    "pdb_id": {
      "description": "PDB identifier (e.g., '1KZK', '2OZR', '4HHB'). Required.",
      "type": "string"
    }
  },
  "required": [
    "pdb_id"
  ],
  "type": "object"
}

Examples (1)

{
  "ligand_bias": false,
  "pdb_id": "1AKI"
}

Identifiers

Catalog ID

tu_ProteinsPlus_predict_binding_sites_v3

Tool name

ProteinsPlus_predict_binding_sites_v3

Added

2026-04-30 22:47Z

Tags

tooluniverse