Rapid and sensitive protein complex alignment with Foldseek-Multimer
Advances in computational structure prediction will vastly augment the hundreds of thousands of currently available protein complex structures. Translating these into discoveries requires aligning them, which is computationally prohibitive. Foldseek-Multimer computes complex alignments from compatible chain-to-chain alignments, identified by efficiently clustering their superposition vectors. Foldseek-Multimer is 3-4 orders of magnitudes faster than the gold standard, while producing comparable alignments; this allows it to compare billions of complex pairs in 11 h. Foldseek-Multimer is open-source software available at GitHub via https://github.com/steineggerlab/foldseek/ , https://search.foldseek.com/search/ and the BFMD database.
Authors
- Johannes Söding (ORCID: https://orcid.org/0000-0001-9642-8244)
- Cameron L. M. Gilchrist (ORCID: https://orcid.org/0000-0001-7798-427X)
- Milot Mirdita (ORCID: https://orcid.org/0000-0001-8637-6719)
- Martin Steinegger (ORCID: https://orcid.org/0000-0001-8781-9753)
- Emmanuel D. Levy (ORCID: https://orcid.org/0000-0001-8959-7365)
- Eli Levy Karin (ORCID: https://orcid.org/0000-0002-5045-0857)
- Hugo Schweke (ORCID: https://orcid.org/0000-0002-7830-1546)
- Woosub Kim (ORCID: https://orcid.org/0009-0005-9356-866X)
Institutions
- University of Geneva (CH)
- Seoul National University (KR)
- National University College (PR)
- Institute of Molecular Biology (AM)
- Max Planck Institute for Multidisciplinary Sciences (DE)
- Weizmann Institute of Science (IL)
- University of Göttingen (DE)
Publication Details
- Journal
- Nature Methods
- Published
- 2025-02-05
- DOI
- https://doi.org/10.1038/s41592-025-02593-7
- Citations
- 46
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 36.27
Funders
- European Bioinformatics Institute
- European Commission
- National Research Foundation
- Seoul National University
- National Research Foundation of Korea
- Université de Genève
- Samsung
- Horizon 2020 Framework Programme