Agent skill · research science · google-deepmind
foldseek-structural-search
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.
Why this skill is useful
Adds specific commands and validation rules for querying the Foldseek API with 3D protein structure files, which the AI wouldn't reliably generate on its own.
What it needs
Requires uv installed locally. About 3k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
Prerequisites 1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH. 2. User Notification: If .licenses/foldseekstructuralsearchLICENSE.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 .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 1. 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). 2. Database Validation: Check if the user requested specific databases to search. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/foldseek_structural_search