Foldseek Tools

Configuration File: foldseek_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

Foldseek_get_result (Type: FoldseekTool)

Get results for a previously submitted Foldseek structure search job by ticket ID. Use this if a …

Foldseek_get_result tool specification

Tool Information:

  • Name: Foldseek_get_result

  • Type: FoldseekTool

  • Description: Get results for a previously submitted Foldseek structure search job by ticket ID. Use this if a search was submitted but results were not yet available. Returns structural alignments if the job is complete, or the current job status if still running.

Parameters:

  • ticket_id (string) (required) Foldseek job ticket ID returned from a previous search submission.

  • max_results (integer) (optional) Maximum number of results to return (default 10, max 50).

Example Usage:

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

Foldseek_search_structure (Type: FoldseekTool)

Search for structurally similar proteins using Foldseek. Given a PDB ID, downloads the structure …

Foldseek_search_structure tool specification

Tool Information:

  • Name: Foldseek_search_structure

  • Type: FoldseekTool

  • Description: 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.

Parameters:

  • pdb_id (string) (optional) PDB ID to search (e.g., ‘4HHB’, ‘1CRN’). The structure will be fetched from RCSB PDB.

  • sequence (string) (optional) Amino acid sequence to search (alternative to pdb_id). For sequence-based structure search. Alias: ‘query’.

  • query (string) (optional) Amino acid sequence to search (alias for sequence).

  • database (string) (optional) 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).

  • mode (string) (optional) Search mode: ‘tmalign’ (fast 3Di+AA, default), ‘tmalign’ (TM-align, slower but more sensitive).

  • max_results (integer) (optional) Maximum number of results to return (default 10, max 50).

Example Usage:

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