Pdbe Search Tools

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

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

Available Tools

PDBeSearch_get_compound (Type: PDBeSearchTool)

Get PDB ligand/compound information by compound ID from PDBe. Returns chemical name, formula, mol…

PDBeSearch_get_compound tool specification

Tool Information:

  • Name: PDBeSearch_get_compound

  • Type: PDBeSearchTool

  • Description: Get PDB ligand/compound information by compound ID from PDBe. Returns chemical name, formula, molecular weight, InChI, InChI key, SMILES, and systematic names. Useful for looking up small molecules that co-crystallize with proteins. Example: ‘ATP’ returns adenosine-5’-triphosphate (C10H16N5O13P3, MW 507.18); ‘HEM’ returns protoporphyrin IX containing iron.

Parameters:

  • compound_id (string) (required) PDB ligand/compound 3-letter code. Examples: ‘ATP’ (adenosine triphosphate), ‘HEM’ (heme), ‘NAG’ (N-acetyl-D-glucosamine), ‘FAD’ (flavin adenine dinucleotide).

Example Usage:

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

PDBeSearch_search_by_organism (Type: PDBeSearchTool)

Search PDB structures filtered by organism through PDBe’s Solr search. Combines keyword search wi…

PDBeSearch_search_by_organism tool specification

Tool Information:

  • Name: PDBeSearch_search_by_organism

  • Type: PDBeSearchTool

  • Description: Search PDB structures filtered by organism through PDBe’s Solr search. Combines keyword search with organism name filtering. Useful for finding species-specific protein structures. Example: searching for ‘kinase’ in ‘Homo sapiens’ returns human protein kinase structures sorted by resolution.

Parameters:

  • organism (string) (required) Scientific name of organism. Examples: ‘Homo sapiens’, ‘Escherichia coli’, ‘Mus musculus’, ‘Saccharomyces cerevisiae’.

  • query ([‘string’, ‘null’]) (optional) Optional keyword query to combine with organism filter. Examples: ‘kinase’, ‘receptor’. Default searches all structures for the organism.

  • limit ([‘integer’, ‘null’]) (optional) Maximum results to return (1-50, default 10).

Example Usage:

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

PDBeSearch_search_structures (Type: PDBeSearchTool)

Search PDB structures through PDBe’s Solr search interface by keyword, protein name, or gene name…

PDBeSearch_search_structures tool specification

Tool Information:

  • Name: PDBeSearch_search_structures

  • Type: PDBeSearchTool

  • Description: Search PDB structures through PDBe’s Solr search interface by keyword, protein name, or gene name. Returns PDB IDs, titles, resolution, experimental methods, deposition dates, and organisms, sorted by resolution (best first). Complements RCSB PDB tools with powerful full-text search. Example: searching ‘insulin’ returns 400+ structures; ‘BRCA1’ returns 148 structures including BRCT domains.

Parameters:

  • query (string) (required) Search query - protein name, gene name, or keyword. Supports Solr syntax. Examples: ‘insulin’, ‘BRCA1’, ‘kinase AND human’, ‘TP53’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum results to return (1-50, default 10).

Example Usage:

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