GPU-accelerated homology search with MMseqs2
Felix Kallenborn, Alejandro Chacón, Christian Hundt, Hassan Sirelkhatim, Kieran Didi, Sooyoung Cha, Christian Dallago, Milot Mirdita, Bertil Schmidt, Martin Steinegger
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/ .