Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer

Overview

Journal Nat Methods

Date 2025 Feb 5

PMID 39910251

Authors

Woosub Kim

Milot Mirdita

Eli Levy Karin

Cameron L M Gilchrist

Hugo Schweke

Johannes Soding

Emmanuel D Levy

Martin Steinegger

Affiliations

Soon will be listed here.

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/ and the BFMD database.

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