Three D Beacons Tools

Configuration File: three_d_beacons_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the three_d_beacons_tools.json configuration file.

Available Tools

ThreeDBeacons_get_structure_summary (Type: ThreeDBeaconsTool)

Get a summary of all available 3D structure models for a protein from the 3D Beacons Hub. Aggrega…

ThreeDBeacons_get_structure_summary tool specification

Tool Information:

  • Name: ThreeDBeacons_get_structure_summary

  • Type: ThreeDBeaconsTool

  • Description: Get a summary of all available 3D structure models for a protein from the 3D Beacons Hub. Aggregates data from multiple providers: PDBe (experimental), AlphaFold DB (AI-predicted), SWISS-MODEL (homology), PED (conformational ensembles), AlphaFill, and isoform.io. Returns total structure count broken down by provider and model category (experimentally determined, template-based, ab-initio, conformational ensemble). Example: P04637 (TP53) returns 327 structures from 6 providers: 299 PDBe experimental, 20 PED ensembles, 4 SWISS-MODEL homology models, plus AlphaFold and AlphaFill predictions.

Parameters:

  • accession (string) (required) UniProt protein accession. Examples: ‘P04637’ (TP53, 327 structures), ‘P00533’ (EGFR, 407 structures), ‘P01308’ (Insulin), ‘P38398’ (BRCA1).

Example Usage:

query = {
    "name": "ThreeDBeacons_get_structure_summary",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

ThreeDBeacons_get_structures (Type: ThreeDBeaconsTool)

Get detailed list of 3D structure models for a protein from the 3D Beacons Hub. Returns individua…

ThreeDBeacons_get_structures tool specification

Tool Information:

  • Name: ThreeDBeacons_get_structures

  • Type: ThreeDBeaconsTool

  • Description: Get detailed list of 3D structure models for a protein from the 3D Beacons Hub. Returns individual structure entries with model identifier, provider, category, coverage, resolution (experimental), confidence score (predicted), and download URL. Supports filtering by category (e.g., ‘EXPERIMENTALLY DETERMINED’) or provider (e.g., ‘AlphaFold DB’). Example: P04637 filtered to ‘TEMPLATE-BASED’ returns 5 structures from SWISS-MODEL and AlphaFill with coverage and sequence range.

Parameters:

  • accession (string) (required) UniProt protein accession. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P01308’ (Insulin).

  • category (string) (optional) Filter by model category. Options: ‘EXPERIMENTALLY DETERMINED’, ‘TEMPLATE-BASED’, ‘AB-INITIO’, ‘CONFORMATIONAL ENSEMBLE’. Case-insensitive partial match.

  • provider (string) (optional) Filter by data provider. Options: ‘PDBe’, ‘AlphaFold DB’, ‘SWISS-MODEL’, ‘PED’, ‘AlphaFill’, ‘isoform.io’. Case-insensitive partial match.

  • max_results (integer) (optional) Maximum structures to return (default 20, max 100).

Example Usage:

query = {
    "name": "ThreeDBeacons_get_structures",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)