Science✦ Official

foldseek-structural-search

### Foldseek Structural Search

google-deepmind/science-skills|Updated Jun 4, 2026

Works with

Claude CodeCursorClineWindsurfCodex

What it does

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, ..."

Repository

google-deepmind/science-skills

Last updated

Jun 4, 2026

Installation Guide

Select your AI agent

How to use foldseek-structural-search on Cursor

AI-first code editor with Composer

Prerequisites

Before installing skills in Cursor, ensure your development environment meets these requirements:

›Cursor installed and configured on your machine
›Node.js 16+ with npm — verify with node --version
›Active project directory where you want to add foldseek-structural-search

Run the install command

Execute the skills CLI command in your project's root directory to begin installation:

$npx skills add https://github.com/google-deepmind/science-skills --skill foldseek-structural-search

Fetches foldseek-structural-search from google-deepmind/science-skills and configures it for Cursor.

Select Cursor when prompted

The CLI shows a list of agents. Use arrow keys and space to select Cursor:

◆ Which agents do you want to install to?

│

│ ── Universal (.agents/skills) ────────────────

│ · Cline · Codex · Goose · Windsurf

│ ●Cursor(selected)

│ · Cursor · Aider · Continue

Verify installation

Confirm successful installation by checking the skill directory location:

.cursor/skills/foldseek-structural-search

Restart Cursor to activate foldseek-structural-search. Access via /foldseek-structural-search in your agent's command palette.

⚠

Security Notice

We perform automated surface-level scans (Gen AI Scanner, Socket, Snyk) during installation. These checks detect common vulnerabilities but do not guarantee complete security. Always review skill source code and verify the publisher's reputation before production use.

Skills execute code in your environment. Always review source, verify the publisher, and test in isolation before production.

›View source on GitHub ›Skills CLI docs ›About Cursor ›What are agent skills?

Documentation

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Use Cases

Task Automation & Efficiency

Automate repetitive workflows and reduce manual effort

Example

Generate reports, summarize documents, draft communications

✓

Save 3-5 hours per week on routine tasks

Knowledge Enhancement

Learn new skills, understand complex topics, get expert guidance

Example

Explain concepts, provide examples, suggest learning resources

✓

Accelerate learning and skill development by 2x

Quality Improvement

Enhance output quality through reviews, suggestions, and refinements

Example

Review drafts, suggest improvements, catch errors

✓

Improve work quality by 30-40% with less effort

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.
Q-Cov (Query Coverage): High percentages mean the match covers the majority of the query protein's overall shape, rather than just a small local motif.
E-value & Seq Identity: Use these to provide additional evolutionary context.

Perform Functional Analysis: Analyze the text descriptions embedded within the Target ID column for the reported matches.

Explicitly report the specific protein names/functions of the top structural homologues.
Provide a synthesized overview summarizing the entire variety of different functions, domains, or protein families found across the whole list of homologues (e.g., "Most hits are portal proteins, but there is also a distinct cluster of viral capsid matches...").

Explicitly inform the user of both newly created files (.json and .md) and their locations so they can be seamlessly used in subsequent analysis steps.

foldseek-structural-search

What it does

Category

Repository

Last updated

Installation Guide

How to use foldseek-structural-search on Cursor

Prerequisites

Run the install command

Select Cursor when prompted

Verify installation

Security Notice

Documentation

List & Monetize Your Skill

Use Cases

Task Automation & Efficiency

Knowledge Enhancement

Quality Improvement

Install Skill

Prerequisites

Goal

Core Rules

Instructions

* If the API returns an error or the file is missing, inform the user clearly

Implementation Guide

Best Practices

When to Use This

Learning Path

Related Skills

pdb-database

alphafold-database-fetch-and-analyze

latex-posters

transformers

efficient-fable

research-paper-writer

Reviews

Discussion

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.