Foldseek Structural Search
Performs 3D structural searches of proteins against various databases (PDB, AlphaFold...
Install
npx skills add google-deepmind/science-skills --skill foldseek-structural-search -g -a claude-code -y- Repository
- google-deepmind/science-skills3.4k
- Category
- Media
- Updated
- 12d ago
- License
- Apache-2.0
- Context cost
- Lightabout 1,231 tokens
- Runs scripts
- Yes, review before use
What it does
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 theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- User Notification: If .licenses/foldseek_structural_search_LICENSE.txt does not already exist in the workspace root 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.mmciffile path. - Strict Validation: Never bypass the input validation or the database allowlist check.
- Do Not Parse the JSON: Rely entirely on the generated
.mdfile 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.
