Rapid and sensitive protein complex alignment with Foldseek-Multimer.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 39910251.
- Also identified by DOI 10.1038/s41592-025-02593-7 and PMC identifier 11903335.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- Software
- Proteins
- Sequence Alignment
- Computational Biology