GPU-accelerated homology search with MMseqs2
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Rapidly growing protein databases demand faster sensitive search tools. Here the graphics processing unit (GPU)-accelerated MMseqs2 delivers 6× faster single-protein searches than CPU methods on 2 × 64 cores, speeds previously requiring large protein batches. For larger query batches, it is the most cost-effective solution, outperforming the fastest alternative method by 2.4-fold with eight GPUs. It accelerates protein structure prediction with ColabFold 31.8× over the standard AlphaFold2 pipeline and protein structure search with Foldseek by 4–27×.
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Nature methods : techniques for life scientists and chemists, 22, Nature, London, 2025, https://doi.org/10.1038/s41592-025-02819-8