ProteinsPlus Analyze Binding Site Similarity

Overview

Analyze binding site similarity and generate structural ensembles using SIENA (Structural Interaction fingerprint for ENsemble Analysis). Performs comprehensive binding site comparison across multiple protein structures to identify similar pockets for ensemble docking, virtual screening, or mutation analysis. Supports multiple modes: flexibility analysis (compare conformations), docking preparation (build ensemble), screening (find similar sites), mutation analysis (assess tolerance), and ligand pose comparison (compare binding modes). Returns aligned structures, binding site similarity scores, and structural ensembles. Critical for accounting for protein flexibility in structure-based drug design, understanding conformational diversity, and improving docking accuracy through ensemble approaches. Example: Use 'screening' mode on 1KZK to find proteins with similar ATP-binding sites.

Status

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

Note: Upstream throttles to ~5 req/min; not exposed to anonymous Try-It.

Last probed

never

Last success

never

Last latency

—

Schema

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

{
  "properties": {
    "flexibility_sensitivity": {
      "description": "Sensitivity for flexibility detection (0.0-1.0). Default: 0.5. Higher = more flexible regions detected. Example: Use 0.7 for highly dynamic proteins.",
      "maximum": 1,
      "minimum": 0,
      "type": "number"
    },
    "fragment_length": {
      "description": "Fragment length for analysis (3-15). Default: 9. Longer fragments = more specific matching. Example: Use 12 for strict similarity.",
      "maximum": 15,
      "minimum": 3,
      "type": "integer"
    },
    "ligand": {
      "description": "Ligand identifier in format 'residue_name_residue_chain_residue_number' (e.g., 'JE2_A_701'). Mutually exclusive with pocket.",
      "type": "string"
    },
    "maximum_mutations": {
      "description": "Maximum number of mutations allowed in mutation analysis mode (0-10). Default: 3. Example: Use 5 for permissive mutation screening.",
      "maximum": 10,
      "minimum": 0,
      "type": "integer"
    },
    "minimal_site_coverage": {
      "description": "Minimum binding site coverage required (0.3-1.0). Default: 0.8. Higher = more complete binding site overlap required. Example: Use 0.9 for stringent matches.",
      "maximum": 1,
      "minimum": 0.3,
      "type": "number"
    },
    "minimal_site_identity": {
      "description": "Minimum binding site sequence identity threshold (0.3-1.0). Default: 0.6. Higher = stricter matching. Example: Use 0.8 for closely related proteins.",
      "maximum": 1,
      "minimum": 0.3,
      "type": "number"
    },
    "mode": {
      "description": "Analysis mode: 'flexibility_analysis' (compare protein conformations), 'docking' (prepare ensemble for docking), 'screening' (find similar binding sites for virtual screening), 'mutation_analysis' (assess mutation tolerance), or 'ligand_pose_comparison' (compare binding poses). Required. Example: Use 'screening' for hit discovery across protein families.",
      "enum": [
        "flexibility_analysis",
        "docking",
        "screening",
        "mutation_analysis",
        "ligand_pose_comparison"
      ],
      "type": "string"
    },
    "pdb_id": {
      "description": "PDB identifier (e.g., '1KZK', '2OZR', '4HHB'). Required.",
      "type": "string"
    },
    "pocket": {
      "description": "Pocket definition for analysis (alternative to ligand). Example: Define custom pocket region. Mutually exclusive with ligand.",
      "type": "string"
    },
    "site_radius": {
      "description": "Radius around ligand to define binding site (3-15 Angstroms). Requires ligand. Default: 6.5. Example: Use 8.0 for larger binding sites.",
      "maximum": 15,
      "minimum": 3,
      "type": "number"
    }
  },
  "required": [
    "pdb_id",
    "mode"
  ],
  "type": "object"
}

Examples (1)

{
  "flexibility_sensitivity": 1,
  "fragment_length": 1,
  "maximum_mutations": 1,
  "minimal_site_coverage": 1,
  "minimal_site_identity": 1,
  "mode": "",
  "pdb_id": "1AKI",
  "site_radius": 1
}

Identifiers

Catalog ID

tu_ProteinsPlus_analyze_binding_site_similarity

Tool name

ProteinsPlus_analyze_binding_site_similarity

Added

2026-04-30 22:47Z

Tags

tooluniverse, slow