Cortexa research tool·structure·foldseek

Foldseek Search Structure

Search for structurally similar proteins using Foldseek. Given a PDB ID, downloads the structure from RCSB and searches against AlphaFold DB (afdb50), PDB100, or other structure databases. Returns structural alignments ranked by e-value. This is an async operation that submits a job and polls for results (typically 10-60 seconds). Example: pdb_id='4HHB' finds proteins with similar 3D fold to hemoglobin.

SlowCortexa

Status

Succeeds, but routinely takes more than 8 seconds. Hidden from the agent's default toolset; available via opt-in.

Note: Async job; submission returns a ticket polled separately via Foldseek_get_result.

Last probed: never
Last success: never
Last latency: —

Schema

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

{
  "properties": {
    "database": {
      "default": "afdb50",
      "description": "Database to search against. Options: 'afdb50' (AlphaFold DB 50% clustered, default), 'afdb-swissprot' (AlphaFold SwissProt), 'afdb-proteome' (AlphaFold proteomes), 'pdb100' (PDB), 'gmgcl_id' (GMGC), 'bfmd' (ESMAtlas), 'cath50' (CATH), 'mgnify_esm30' (MGnify ESM).",
      "type": "string"
    },
    "max_results": {
      "default": 10,
      "description": "Maximum number of results to return (default 10, max 50).",
      "type": "integer"
    },
    "mode": {
      "default": "3diaa",
      "description": "Search mode: 'tmalign' (fast 3Di+AA, default), 'tmalign' (TM-align, slower but more sensitive).",
      "type": "string"
    },
    "pdb_id": {
      "description": "PDB ID to search (e.g., '4HHB', '1CRN'). The structure will be fetched from RCSB PDB.",
      "type": "string"
    },
    "query": {
      "description": "Amino acid sequence to search (alias for sequence).",
      "type": "string"
    },
    "sequence": {
      "description": "Amino acid sequence to search (alternative to pdb_id). For sequence-based structure search. Alias: 'query'.",
      "type": "string"
    }
  },
  "required": [],
  "type": "object"
}

Examples (1)

Default Foldseek Search Structure call

input

{
  "max_results": 1,
  "pdb_id": "1AKI",
  "query": "BRCA1"
}

Expected response keys: success

Identifiers

Catalog ID: tu_Foldseek_search_structure
Tool name: Foldseek_search_structure
Added: 2026-04-30 22:47Z
Tags: tooluniverse, slow

Foldseek Search Structure

SlowCortexa

Schema

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

{ "properties": { "database": { "default": "afdb50", "description": "Database to search against. Options: 'afdb50' (AlphaFold DB 50% clustered, default), 'afdb-swissprot' (AlphaFold SwissProt), 'afdb-proteome' (AlphaFold proteomes), 'pdb100' (PDB), 'gmgcl_id' (GMGC), 'bfmd' (ESMAtlas), 'cath50' (CATH), 'mgnify_esm30' (MGnify ESM).", "type": "string" }, "max_results": { "default": 10, "description": "Maximum number of results to return (default 10, max 50).", "type": "integer" }, "mode": { "default": "3diaa", "description": "Search mode: 'tmalign' (fast 3Di+AA, default), 'tmalign' (TM-align, slower but more sensitive).", "type": "string" }, "pdb_id": { "description": "PDB ID to search (e.g., '4HHB', '1CRN'). The structure will be fetched from RCSB PDB.", "type": "string" }, "query": { "description": "Amino acid sequence to search (alias for sequence).", "type": "string" }, "sequence": { "description": "Amino acid sequence to search (alternative to pdb_id). For sequence-based structure search. Alias: 'query'.", "type": "string" } }, "required": [], "type": "object" }