| name | foldseek-structural-search |
| description | Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.
|
Prerequisites
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.- User Notification: If LICENSE_NOTIFICATION.txt does not already exist in
this skill directory then (1) prominently notify the user to check the terms
at https://search.foldseek.com/search and
https://github.com/steineggerlab/foldseek, then (2) create the file
recording the notification text and timestamp.
Goal
Submit a user-provided 3D protein structure file (.cif, .mmcif, or .pdb)
to the Foldseek web server API to find structurally similar proteins. Report the
top structural hits, interpret key alignment metrics, summarize the inferred
protein functions, save the Markdown-formatted table to a .md file, and save
the full detailed results to a local JSON file.
Core Rules
- File Requirement: This tool absolutely cannot search by sequence, name,
or accession ID. It strictly requires a
.pdb, .cif, or .mmcif file
path.
- Strict Validation: Never bypass the input validation or the database
allowlist check.
- Do Not Parse the JSON: Rely entirely on the generated
.md file for
your immediate summary. The JSON is saved purely for subsequent, specialized
tool use.
- No Raw Parsing: Do not attempt to parse or read the raw 3D coordinates
yourself; always pass the file to the script.
- Notification: If this skill is used, ensure this is mentioned in the
output.
Instructions
- Strict Input Validation: Verify that the user has explicitly provided a
valid path to a
.cif, .mmcif, or .pdb file in their workspace.
- If the user provided a protein name, an amino acid sequence, or an
accession ID (e.g., a UniProt ID) but NO downloaded structure file,
halt immediately. Do not run the script.
- Inform the user that Foldseek requires a physical 3D coordinate file,
and suggest downloading the structure first (e.g., using the AlphaFold
fetch tool).
- Database Validation: Check if the user requested specific databases to
search.
- Allowed List:
afdb50, afdb-swissprot, pdb100, BFVD,
mgnify_esm30, cath50, gmgcl_id, bfmd, afdb-proteome.
- If the user requests a database NOT on this list, halt immediately.
Do not run the script. Inform the user that the database is unsupported
and provide them with the allowed list.
- Generate File Names: Generate descriptive output file names for both the
JSON data and the Markdown table based on the input file (e.g.,
proteinA_foldseek_results.json and proteinA_foldseek_results.md).
- Execute the python script based on the user's request, redirecting the
standard output into your generated
.md file:
- Default (No databases specified):
uv run scripts/search.py <path-to-file> -o <generated-filename.json> > <generated-filename.md>
- Custom (Valid databases specified):
uv run scripts/search.py <path-to-file> -o <generated-filename.json> --databases <db1,db2,db3> > <generated-filename.md>
- The script will query the databases, save the full JSON payload, and write a
Markdown-formatted table to your specified
.md file.
- Read the Results: Open and read the newly generated
.md file carefully
to view the Markdown table.
- Interpret the Metrics: Summarize the top 3 to 5 structural matches that
have meaningfull annotations for the user. When reporting, assess the match
quality using these specific fields:
- Prob (Probability): Values approaching 1.0 (100%) indicate extreme
confidence that the fold is a true structural homologue.
* If the API returns an error or the file is missing, inform the user clearly
and ask them to verify the file path.
