Rcsb Search Tools#

Configuration File: rcsb_search_tools.json Tool Type: Local Tools Count: 1

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

Available Tools#

PDB_search_similar_structures (Type: RCSBSearchTool)#

Search RCSB PDB by protein sequence, strict structure-shape matching, or text. Results use exact …

PDB_search_similar_structures tool specification

Tool Information:

  • Name: PDB_search_similar_structures

  • Type: RCSBSearchTool

  • Description: Search RCSB PDB by protein sequence, strict structure-shape matching, or text. Results use exact offset pagination: continue with next_start while has_more is true. Sequence identity cutoff is applied only to sequence search; structure search explicitly reports similarity_threshold_applied=false because the official strict_shape_match request has no numeric threshold. Text-result GraphQL enrichment reports its own completeness and missing IDs.

Parameters:

  • query (string) (required) PDB ID (e.g., ‘1ABC’), protein sequence (amino acids), or search text (e.g., drug name, protein name, keyword). For structure search, provide PDB ID. For sequence search, provide amino acid sequence. For text search, provide drug name, protein name, or keyword.

  • search_type (string) (optional) Type of search: ‘sequence’ for sequence-based similarity search, ‘structure’ for structure-based similarity search using PDB ID, ‘text’ for text-based search by name or keyword

  • similarity_threshold (number) (optional) Sequence identity cutoff from 0 to 1. Applied only for sequence search. RCSB strict structure-shape search has no numeric threshold, so structure responses explicitly report similarity_threshold_applied=false.

  • max_results (integer) (optional) Number of results per page (1-100). Invalid values are rejected rather than silently clamped.

  • start (integer) (optional) Zero-based result offset using RCSB’s official paginate.start parameter. Continue with data.next_start while data.has_more is true.

Example Usage:

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