Sabdab Tools

Configuration File: sabdab_tools.json Tool Type: Local Tools Count: 4

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

Available Tools

SAbDab_get_structure (Type: SAbDabTool)

Get antibody structure details from SAbDab by PDB ID. Returns CDR annotations, chain information,…

SAbDab_get_structure tool specification

Tool Information:

  • Name: SAbDab_get_structure

  • Type: SAbDabTool

  • Description: Get antibody structure details from SAbDab by PDB ID. Returns CDR annotations, chain information, and antigen binding data. Useful for structural analysis of antibody-antigen complexes.

Parameters:

  • operation (string) (optional) No description

  • pdb_id (string) (optional) 4-character PDB ID (e.g., 1IGT, 6W41). Alias: pdb_code.

  • pdb_code (string) (optional) Alias for pdb_id. 4-character PDB ID (e.g., 1IGT, 6W41).

Example Usage:

query = {
    "name": "SAbDab_get_structure",
    "arguments": {
    }
}
result = tu.run(query)

SAbDab_get_structure_summary (Type: SAbDabTool)

Get per-structure curated antibody annotations from SAbDab for a PDB ID. Returns the SAbDab summa…

SAbDab_get_structure_summary tool specification

Tool Information:

  • Name: SAbDab_get_structure_summary

  • Type: SAbDabTool

  • Description: Get per-structure curated antibody annotations from SAbDab for a PDB ID. Returns the SAbDab summary TSV row(s): antigen name/type/species, heavy/light chain species and IMGT V-gene subclass, resolution, experimental method, R-free / R-factor, scFv and engineered flags, and (when curated) binding affinity Kd, delta_G, affinity method, temperature and PMID. Use for antibody-antigen complex characterization. Pass a 4-character PDB ID (e.g., 7d6i, 3hfm). No authentication required.

Parameters:

  • operation (string) (optional) No description

  • pdb_id (string) (optional) 4-character PDB ID of an antibody structure (e.g., ‘7d6i’, ‘3hfm’). Aliases: pdb_code, pdb.

  • pdb_code (string) (optional) Alias for pdb_id.

  • pdb (string) (optional) Alias for pdb_id.

Example Usage:

query = {
    "name": "SAbDab_get_structure_summary",
    "arguments": {
    }
}
result = tu.run(query)

SAbDab_get_summary (Type: SAbDabTool)

Get SAbDab database summary and statistics. Returns information about database content, features,…

SAbDab_get_summary tool specification

Tool Information:

  • Name: SAbDab_get_summary

  • Type: SAbDabTool

  • Description: Get SAbDab database summary and statistics. Returns information about database content, features, and access URLs. Good starting point for exploring antibody structural data.

Parameters:

  • operation (string) (optional) No description

Example Usage:

query = {
    "name": "SAbDab_get_summary",
    "arguments": {
    }
}
result = tu.run(query)

SAbDab_search_structures (Type: SAbDabTool)

Search SAbDab structural antibody database. Returns a direct browse URL to matching antibody stru…

SAbDab_search_structures tool specification

Tool Information:

  • Name: SAbDab_search_structures

  • Type: SAbDabTool

  • Description: Search SAbDab structural antibody database. Returns a direct browse URL to matching antibody structures — SAbDab’s search endpoint does not expose a JSON API, so use SAbDab_get_structure with a known PDB ID for structured data. Tip: retrieve the full SAbDab summary TSV from https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/summary/?all=true for bulk filtering.

Parameters:

  • operation (string) (optional) No description

  • query (string) (optional) Search query - antigen name, species, or keywords (e.g., ‘HER2’, ‘anti-CD20’)

  • antigen (string) (optional) Alias for query. Antigen name to search (e.g., ‘EGFR’, ‘HER2’).

  • limit (integer) (optional) Maximum results (default: 50)

Example Usage:

query = {
    "name": "SAbDab_search_structures",
    "arguments": {
    }
}
result = tu.run(query)