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.
| Requirement | Minimum | Recommended |
|---|---|---|
| RAM | 8GB | 16GB |
| Disk | 10GB | 50GB (local databases) |
No GPU required.
curl -X POST "https://search.foldseek.com/api/ticket" \
-F "[email protected]" \
-F "database[]=afdb50" \
-F "database[]=pdb100"
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/
| Parameter | Default | Description |
|---|---|---|
--min-seq-id | 0.0 | Minimum sequence identity |
-e | 0.001 | E-value threshold |
--alignment-type | 2 | 0=3Di, 1=TM, 2=3Di+AA |
| Database | Description | Size |
|---|---|---|
pdb100 | PDB clustered at 100% | ~200K structures |
afdb50 | AlphaFold DB at 50% | ~67M structures |
swissprot | SwissProt structures | ~500K structures |
foldseek easy-search design.pdb afdb50 novelty.m8 tmp/
# Novel if: top hit identity < 30%
foldseek easy-search design.pdb pdb100 similar_natural.m8 tmp/
foldseek easy-search motif.pdb pdb100 scaffolds.m8 tmp/ \
--min-seq-id 0.0 -e 10
Searching by?
├─ 3D structure → Foldseek ✓
├─ Sequence → Use BLAST (uniprot skill)
└─ Both → Run both, compare results
| Error | Cause | Fix |
|---|---|---|
| No hits | Too strict cutoff | Lower e-value, try larger database |
Database not found | Wrong path | Check database location |
| Out of memory | Large database | Use web server |
Next: Download hits with pdb skill → use for scaffold design.