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) for antibody structures by the antigen they bind, an…

SAbDab_search_structures tool specification

Tool Information:

  • Name: SAbDab_search_structures

  • Type: SAbDabTool

  • Description: Search SAbDab (Structural Antibody Database) for antibody structures by the antigen they bind, antibody source organism, experimental method, resolution, antigen type or antibody format. Returns one compact row per antibody instance: PDB ID, structure name, antibody format, resolution, heavy and light chain CDR1-3 with V/J genes, and the bound antigen instance IDs. ‘query’ is matched as a case-insensitive substring of the antigen’s name as deposited in the PDB, at most 25 characters: gene symbols and shorthand usually miss (‘HER2’ and ‘PD-1’ find nothing), so use a distinctive part of the full protein name (‘erbB-2’, ‘cell death protein 1’, ‘spike glycoprotein’, ‘lysozyme’). Results are paginated: data.total_matches is the full count, data.count is the rows on this page, and data.next_offset continues while data.has_more is true. Use SAbDab_get_structure_summary with a returned pdb_id for the full entry.

Parameters:

  • operation (string) (optional) No description

  • query (string) (optional) Part of the bound antigen’s name as deposited in the PDB, case-insensitive, at most 25 characters (e.g. ‘erbB-2’, ‘lysozyme’, ‘spike glycoprotein’). Gene symbols such as ‘HER2’ usually match nothing. Omit to list all antibody instances matching the other filters.

  • antigen (string) (optional) Alias for query.

  • limit (integer) (optional) Rows per page (1-100, default 20).

  • species (string) (optional) Substring of the antibody’s source organism scientific name (e.g. ‘Homo sapiens’, ‘Lama glama’).

  • method (string) (optional) Experimental method of the structure (case-insensitive).

  • resolution_max (number) (optional) Keep structures determined at this resolution (angstroms) or better.

  • antigen_type (string) (optional) Kind of antigen bound (case-insensitive).

  • antibody_type (string) (optional) Antibody format: FV, FAB, FAB+FC, FV*, SD-H (heavy-chain single domain, e.g. nanobody), SD-L or VNAR (case-insensitive).

  • pdb_id (string) (optional) Restrict to one PDB entry (4-character code, e.g. ‘3hfm’).

  • offset (integer) (optional) Zero-based row offset; continue with data.next_offset while data.has_more is true.

Example Usage:

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