foldseek

name: foldseek description: > 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. license: MIT category: utilities tags: [search, structure, database, similarity] source: https://github.com/adaptyvbio/protein-design-skills

Foldseek Structure Search

Prerequisites

No GPU required.

How to run

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

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

Option 2: Local installation

conda install -c conda-forge -c bioconda foldseek

# Search PDB
foldseek easy-search query.pdb /path/to/pdb100 results.m8 tmp/

# Search AlphaFold DB
foldseek easy-search query.pdb /path/to/afdb50 results.m8 tmp/

Key Parameters

Databases

Common Use Cases

Novelty check

foldseek easy-search design.pdb afdb50 novelty.m8 tmp/
# Novel if: top hit identity < 30%

Find similar natural structures

foldseek easy-search design.pdb pdb100 similar_natural.m8 tmp/

Scaffold search for motif grafting

foldseek easy-search motif.pdb pdb100 scaffolds.m8 tmp/ \
  --min-seq-id 0.0 -e 10

Decision Tree

Searching by?
├─ 3D structure → Foldseek ✓
├─ Sequence → Use BLAST (uniprot skill)
└─ Both → Run both, compare results

Troubleshooting

Next: Download hits with pdb skill → use for scaffold design.