Foldseek

Foldseek is a Data skill for Claude Code, published by BioTender-max in awesome-bio-agent-skills.

174 stars30 forkson BioTender-max/awesome-bio-agent-skillsAdded 2026/09/07+1% in starsRepository updated 2026/07/01

agent-skillsai-agentai-agentsawesomeawesome-listbioinformaticsbiomedicalclaudeclaude-codeclaude-skillscomputational-biologydrug-discoverygenomicsllmmcpprotein-designproteomicssingle-cellskillstranscriptomics

Install in seconds

Install Foldseek

Copy Foldseek into your Claude Code skills folder. Run the command in your terminal, or review the source on GitHub before installing.

terminal

npx degit https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/adaptyv/foldseek ~/.claude/skills/foldseek

Requires Node.js. Downloads this skill only — not the rest of the repository — into your Claude Code skills folder.

Without Node.js

git clone https://github.com/BioTender-max/awesome-bio-agent-skills.git

Clones the whole repository, then copy the skill’s own directory into your skills folder yourself.

In this catalog

Source file: skills/adaptyv/foldseek/SKILL.md in BioTender-max/awesome-bio-agent-skills
Installs to: ~/.claude/skills/foldseek
Collection: One of 25 skills cataloged from this repository
Category: Data — 796 skills

What Foldseek does

Foldseek searches protein 3D structures for similar folds, structural homologs, and remote homologs. Use it to query PDB, AlphaFold, or other structure databases and to cluster structures by similarity.

Foldseek is cataloged under Data on DirSkills. Foldseek comes from a repository tagged agent-skills, ai-agent, ai-agents, awesome and awesome-list.

Documentation

README

Excerpt

Foldseek Structure Search

Prerequisites

Requirement	Minimum	Recommended
Python	3.8+	3.10
RAM	8GB	16GB
Disk	10GB	50GB (for local databases)

How to run

Note: Foldseek can run locally or via web server. No GPU required.

Option 1: Web Server (Quick; rate-limited, use sparingly)

# Upload structure to web server
curl -X POST "https://search.foldseek.com/api/ticket" \
  -F "q=@query.pdb" \
  -F "database[]=afdb50" \
  -F "database[]=pdb100"

This is the opening of the README. Read the full README on GitHub.

Frequently asked about Foldseek

What else does BioTender-max publish alongside Foldseek?
Foldseek is one of 25 skills that DirSkills catalogs from BioTender-max/awesome-bio-agent-skills, the repository it ships in. Its siblings there include ATAC Seq, AlphaFold and BindCraft Binder Design. Each one is a separate skill with its own page in this directory, installs the same way Foldseek does, and is maintained by BioTender-max in that same repository. The rest of the collection is listed on the BioTender-max/awesome-bio-agent-skills page.
How does Foldseek compare to other Data skills?
Foldseek ranks #748 by stars among the 796 Data skills in this catalog. The most-starred ones next to it are Benchmark Methodology, Jupyter Notebook and Solana. DirSkills ranks by the star count of the repository each skill ships in, so that order reflects how popular those repositories are rather than any review of Foldseek against them. Open each page to compare what they document and how they install.