Computational study demonstrates rapid protein complex alignment in massive structural datasets, highlighting scalable discovery across protein interactomes.
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; allowing it to compare billions of complex-pairs in 11 hours. Foldseek-Multimer is open-source software: github.com/steineggerlab/foldseek , webserver: search.foldseek.com and the BFMD database.
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Kim et al. (2024) studied this question.
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