foldseek
✓Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.
Installation
SKILL.md
| Python | 3.8+ | 3.10 | | RAM | 8GB | 16GB | | Disk | 10GB | 50GB (for local databases) |
Note: Foldseek can run locally or via web server. No GPU required.
| --min-seq-id | 0.0 | Minimum sequence identity | | -e | 0.001 | E-value threshold | | --alignment-type | 2 | 0=3Di, 1=TM, 2=3Di+AA | | --max-seqs | 300 | Max hits to pass through prefilter; reducing this affects sensitivity |
Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz. Source: adaptyvbio/protein-design-skills.
Facts (cite-ready)
Stable fields and commands for AI/search citations.
- Install command
npx skills add https://github.com/adaptyvbio/protein-design-skills --skill foldseek- Category
- </>Dev Tools
- Verified
- ✓
- First Seen
- 2026-02-01
- Updated
- 2026-02-18
Quick answers
What is foldseek?
Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz. Source: adaptyvbio/protein-design-skills.
How do I install foldseek?
Open your terminal or command line tool (Terminal, iTerm, Windows Terminal, etc.) Copy and run this command: npx skills add https://github.com/adaptyvbio/protein-design-skills --skill foldseek Once installed, the skill will be automatically configured in your AI coding environment and ready to use in Claude Code or Cursor
Where is the source repository?
https://github.com/adaptyvbio/protein-design-skills
Details
- Category
- </>Dev Tools
- Source
- skills.sh
- First Seen
- 2026-02-01