Rapid and sensitive protein complex alignment with Foldseek-Multimer

Kim, Woosub; Mirdita, Milot; Karin, Eli Levy; Gilchrist, Cameron L. M.; Schweke, Hugo; Söding, Johannes; Levy, Emmanuel D.; Steinegger, Martin

doi:10.1038/s41592-025-02593-7

articleNature MethodsFeb 5, 2025HYBRID OA

Rapid and sensitive protein complex alignment with Foldseek-Multimer

WKWoosub Kim MMMilot Mirdita ELEli Levy Karin CLCameron L. M. Gilchrist HSHugo Schweke

Seoul National University · University of Geneva · +5 more institutions

PubMed

Indexed incrossrefpubmed

Abstract

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/…

Citation impact

53

total citations

FWCI: 32.04
Percentile: 100%
References: 35

Citations per year

Authors

8

Topics & keywords

Topics

Keywords

Computer science
Cluster analysis
Superposition principle
Software
Computational biology
Theoretical computer science
Data mining
Programming language

No related works found for this paper.