# Foldseek Structural Search

Performs 3D structural searches of proteins against various databases (PDB, AlphaFold...

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Media
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill foldseek-structural-search -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill foldseek-structural-search -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill foldseek-structural-search -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill foldseek-structural-search -g -a gemini-cli -y`

## 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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## 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/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 `.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

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/foldseek_structural_search/SKILL.md