Foldseek Structural Search

This one submits protein structure files to the Foldseek web API and finds structurally similar proteins in their database. You feed it a .cif, .mmcif, or .pdb file and get back a ranked list of structural matches with alignment metrics, plus it saves both a readable Markdown table and the full JSON response locally. Built by Google DeepMind's science team, so the implementation is solid. The license notification workflow is a nice touch, prompting users to check terms before first use. Most useful when you've got an experimental or predicted structure and want to know what other proteins fold the same way, which can give you functional clues even without sequence similarity.

skills.sh installs: 2.2K
GitHub stars: 3.4K
last updated: Aug 21, 2026

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Install

$ npx -y skills add google-deepmind/science-skills --skill foldseek-structural-search --agent claude-code

Installs into .claude/skills of the current project.

Files

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is 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.