Three D Beacons Tools#

Configuration File: three_d_beacons_tools.json Tool Type: Local Tools Count: 3

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

Available Tools#

ThreeDBeacons_get_annotations (Type: ThreeDBeaconsTool)#

Get residue-level structural and functional annotations mapped onto a protein’s 3D models from th…

ThreeDBeacons_get_annotations tool specification

Tool Information:

  • Name: ThreeDBeacons_get_annotations

  • Type: ThreeDBeaconsTool

  • Description: Get residue-level structural and functional annotations mapped onto a protein’s 3D models from the 3D Beacons Hub, with the exact residue and region lists plus source/evidence. This is distinct from the model-list summary: it returns features such as DOMAIN, BINDING, ACT_SITE, METAL, DISULFID, MOD_RES, HELIX, STRAND, INTERFACE, CHANNEL, each carrying a description (with InterPro IDs where applicable), source_name (e.g. InterPro), evidence level (e.g. COMPUTATIONAL/PREDICTED), the list of residue numbers, and start/end regions. Example: P38398 (BRCA1) type=DOMAIN returns the ‘BRCA1-associated (IPR031099)’ domain over residues 7-99.

Parameters:

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

  • type (string) (required) Annotation type to filter to – required by the upstream 3D Beacons API (it 422s without it, confirmed live). Valid values: CARBOHYD, DOMAIN, ACT_SITE, METAL, BINDING, NON_STD, MOD_RES, DISULFID, MUTAGEN, HELIX, STRAND, DISORDERED, INTERFACE, CHANNEL.

  • provider ([‘string’, ‘null’]) (optional) Optional model provider to source annotations from: ‘pdbe’ or ‘alphafold’.

Example Usage:

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

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 3D structure models for a protein from the 3D Beacons Hub. Returns model identifier,…

ThreeDBeacons_get_structures tool specification

Tool Information:

  • Name: ThreeDBeacons_get_structures

  • Type: ThreeDBeaconsTool

  • Description: Get detailed 3D structure models for a protein from the 3D Beacons Hub. Returns model identifier, provider, category, coverage, resolution or confidence, and download URL. Supports category/provider filters and recoverable offset pagination. Continue with next_offset while has_more is true; broad proteins can have hundreds of structures (P04637 currently has more than 300).

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 on this page (default 20).

  • offset (integer) (optional) Zero-based offset in the complete filtered structure list. Continue with data.next_offset.

Example Usage:

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