%0 Journal Article
%T Rapid and sensitive protein complex alignment with Foldseek-Multimer
%U https://www.nature.com/articles/s41592-025-02593-7
%X 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.
%G en
%J Nature Methods
%A Kim, Woosub
%A Mirdita, Milot
%A Levy Karin, Eli
%A Gilchrist, Cameron L. M.
%A Schweke, Hugo
%A Söding, Johannes
%A Levy, Emmanuel D.
%A Steinegger, Martin
%D 2025-02-05