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bioRxiv · 10.1101/2024.11.13.623350

GPU-accelerated homology search with MMseqs2

Kallenborn, F.·Chacon, A.·Hundt, C.·Sirelkhatim, H.·Didi, K.·Dallago, C.·Mirdita, M.·Schmidt, B.·Steinegger, M.
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Abstract

Rapidly growing protein databases demand faster sensitive sequence similarity detection. We present GPU-accelerated search utilizing intra-query parallelization delivering 6x faster single-protein searches compared to state-of-the-art CPU methods on 2x64 cores--speeds previously requiring large protein batches. It is most cost effective, including in large-batches at 0.45x MMseqs2-CPU speed (8 GPUs delivering 2.4x). It accelerates ColabFold structure prediction 31.8x compared to AlphaFold2 and Foldseek search 4-27x. MMseqs2-GPU is open-source at mmseqs.com.

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Kallenborn, F., Chacon, A., Hundt, C., Sirelkhatim, H., Didi, K., Dallago, C., Mirdita, M., Schmidt, B., Steinegger, M.. 2024-11-15. GPU-accelerated homology search with MMseqs2. https://doi.org/10.1101/2024.11.13.623350

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