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<p>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 <a href="https://github.com/steineggerlab/foldseek/">https://github.com/steineggerlab/foldseek/</a>, <a href="https://search.foldseek.com/search">https://search.foldseek.com/search/</a> and the BFMD database.</p>

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Rapid and sensitive protein complex alignment with Foldseek-Multimer

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年2月5日

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

摘要

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.