GPU-accelerated homology search with MMseqs2.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 40968302.
- Also identified by DOI 10.1038/s41592-025-02819-8 and PMC identifier 12510879.
- 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
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×. MMseqs2-GPU is available under an open-source license at https://mmseqs.com/ .
Medical subject headings
- Software
- Computer Graphics
- Computational Biology
- Proteins