Cortexa research tool·structure·rcsb_search

PDB Search Similar Structures

Search for protein structures similar to a given PDB ID or sequence using RCSB PDB structure similarity search. Supports sequence-based, structure-based, and text-based search. Suitable for antibodies, proteins, and other biologics. Use text search to find PDB IDs by drug name, protein name, or keywords.

Livelast probed 2026-04-30 23:07Z· 106msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 106ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "max_results": {
      "default": 20,
      "description": "Maximum number of results to return (1-100). Values outside this range will be clamped.",
      "type": "integer"
    },
    "query": {
      "description": "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.",
      "type": "string"
    },
    "search_type": {
      "default": "sequence",
      "description": "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",
      "enum": [
        "sequence",
        "structure",
        "text"
      ],
      "type": "string"
    },
    "similarity_threshold": {
      "default": 0.7,
      "description": "Similarity threshold (0-1). Higher values return more similar structures. Values outside 0-1 will be clamped. For sequence search, this is the identity cutoff. For structure search, this is the structure similarity threshold. Not used for text search.",
      "type": "number"
    }
  },
  "required": [
    "query"
  ],
  "type": "object"
}

Examples (1)

Default PDB Search Similar Structures call

public-safeinput

{
  "max_results": 1,
  "query": "BRCA1",
  "similarity_threshold": 1
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_PDB_search_similar_structures
Tool name: PDB_search_similar_structures
Added: 2026-04-30 22:47Z
Tags: tooluniverse

PDB Search Similar Structures

Livelast probed 2026-04-30 23:07Z· 106msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "max_results": { "default": 20, "description": "Maximum number of results to return (1-100). Values outside this range will be clamped.", "type": "integer" }, "query": { "description": "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.", "type": "string" }, "search_type": { "default": "sequence", "description": "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", "enum": [ "sequence", "structure", "text" ], "type": "string" }, "similarity_threshold": { "default": 0.7, "description": "Similarity threshold (0-1). Higher values return more similar structures. Values outside 0-1 will be clamped. For sequence search, this is the identity cutoff. For structure search, this is the structure similarity threshold. Not used for text search.", "type": "number" } }, "required": [ "query" ], "type": "object" }