# steineggerlab/foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

Repository: https://github.com/steineggerlab/foldseek
Canonical: https://ross.abutalabs.com/products/foldseek
Homepage: https://foldseek.com
Language: C
License: GPL-3.0
License Family: copyleft
Topics: protein-structure, alignments, bioinformatics, clustering
Last push: 2026-08-24T10:51:23+00:00

## Health v2 (maintenance only)
Score: 67/100 (v2, computed 2026-09-02T17:46:02.011165+00:00)
- activity 99, release rhythm 8, longevity 100
- inputs: {"age_days": 2781, "days_push": 9, "days_rel": 591, "gap_med": null, "n_releases_24m": 1}
- flags: none
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1283, forks 157 (observed 2026-08-28T04:04:14.451121+00:00)

## What it is
Foldseek is a command-line tool for fast and sensitive comparison, search, and clustering of large protein 3D structure sets, including monomer and multimer (complex) searches. It runs on CPU with optional GPU acceleration and can compare proteins directly from sequences using a language model without precomputed structures.

## Use cases
- search a protein structure database for structural homologs
- cluster large sets of predicted protein structures
- align protein complexes with Foldseek-Multimer
- compare protein structures from sequence only using a language model
- find structural similarities across the protein universe at scale
- accelerate structure search with GPU support

## When to choose
- you need to search or cluster millions of protein structures quickly
- you want sensitive structure alignment from the command line or a cluster
- you need monomer and protein-complex (multimer) structural comparisons
- you want sequence-based structural comparison without precomputed structures

## When to avoid
- you only need sequence similarity search without structural context (use BLAST or MMseqs2)
- you need a GUI-only workflow (though a webserver exists, the core tool is CLI)
- you work outside structural biology and protein analysis

## Facets
- artifact type: cli-tool
- maturity: active
- function: search-engine, gpu-computing
- domain: bioinformatics, data-science
- platform: cli, cloud
- tags: protein-structure, structure-alignment, structural-bioinformatics, protein-clustering, multimer-search, protein-language-model, high-performance-computing, clustering, algorithms, linux, macos, docker

## Member repositories
- steineggerlab/foldseek (main) score 67

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:04:14.451121+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T04:57:04.863120+00:00, confidence not recorded.
  - readme: https://github.com/steineggerlab/foldseek (fetched 2026-08-28T04:04:14.451121+00:00, sha 8ce2841d0946)
  - homepage: https://foldseek.com (fetched 2026-08-29T12:12:38.877950+00:00, sha 50aeb2e0083d)
- Data as of 2026-08-30T08:39:29.467469+00:00.