Cortexa research tool·structure·rcsb_advanced_search

RCSBAdvSearch Search By Motif

Search RCSB PDB for protein structures containing a specific sequence motif pattern. Supports PROSITE patterns, regular expressions, and simple patterns. Useful for finding structures with specific functional motifs like zinc fingers, kinase domains, or any sequence pattern of interest. Returns polymer entity identifiers (PDB_ID + entity number).

Livelast probed 2026-04-30 23:07Z· 96msCortexa

Status

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

Last probed: 1d ago
Last success: 1d ago
Last latency: 96ms

Schema

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

{
  "properties": {
    "pattern": {
      "description": "Sequence motif pattern. PROSITE format examples: 'C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H' (zinc finger), 'G-x(4)-GK-[ST]' (P-loop NTP binding). Regex format: 'C.{2,4}C.{3}[LIVMFYWC].{8}H.{3,5}H'. Simple format: 'CXXCXXXH' (X=any amino acid).",
      "type": "string"
    },
    "pattern_type": {
      "description": "Pattern format: 'prosite' (default, PROSITE-style), 'regex' (regular expression), 'simple' (X=any).",
      "type": "string"
    },
    "rows": {
      "description": "Number of results to return (default: 10, max: 50).",
      "type": "integer"
    },
    "sequence_type": {
      "description": "Sequence type: 'protein' (default) or 'dna' or 'rna'.",
      "type": "string"
    }
  },
  "required": [
    "pattern"
  ],
  "type": "object"
}

Examples (1)

Default RCSBAdvSearch Search By Motif call

public-safeinput

{
  "pattern": "",
  "rows": 1
}

Expected response keys: success

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

Identifiers

Catalog ID: tu_RCSBAdvSearch_search_by_motif
Tool name: RCSBAdvSearch_search_by_motif
Added: 2026-04-30 22:47Z
Tags: tooluniverse

RCSBAdvSearch Search By Motif

Livelast probed 2026-04-30 23:07Z· 96msCortexa

Schema

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

{ "properties": { "pattern": { "description": "Sequence motif pattern. PROSITE format examples: 'C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H' (zinc finger), 'G-x(4)-GK-[ST]' (P-loop NTP binding). Regex format: 'C.{2,4}C.{3}[LIVMFYWC].{8}H.{3,5}H'. Simple format: 'CXXCXXXH' (X=any amino acid).", "type": "string" }, "pattern_type": { "description": "Pattern format: 'prosite' (default, PROSITE-style), 'regex' (regular expression), 'simple' (X=any).", "type": "string" }, "rows": { "description": "Number of results to return (default: 10, max: 50).", "type": "integer" }, "sequence_type": { "description": "Sequence type: 'protein' (default) or 'dna' or 'rna'.", "type": "string" } }, "required": [ "pattern" ], "type": "object" }