Foldseek

secondsPaperCodeProduction Ready

Ultra-fast protein structure search, multimer search, and clustering

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_pass
Storage: <5
Strategy: validated; official Foldseek Linux binary with real RCSB PDB benchmark structures
Next: Expose structure upload and database selector; add PDB/AlphaFold DB indexes when larger database storage policy is chosen.

Official Foldseek binary installed; Slurm easy-search benchmark against real RCSB 1CRN/1UBQ structure database completed in 0.688s and produced CSV/TSV/summary artifacts. Large public structure databases remain a scaling task.