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GPU-accelerated homology search with MMseqs2
Open accessPreprint — published as 10.1038/s41592-025-02819-8
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 2×64 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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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Self-citationAccurate structure prediction of biomolecular interactions with AlphaFold 3
Abramson, J., Adler, J., Dunger, J., Evans, R., Green, T., Pritzel, A., Ronneberger, O., Willmore, L., Ballard, A. J., Bambrick, J., et al. (2024) · Nature · doi:10.1038/s41586-024-07487-w · Cited by 15,861
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Research works printed but not linked: 37
- 10.1006/jmbi.1990.9999 · DOI · Paper page
- 10.1371/journal.pcbi.1002195 · DOI · Paper page
- 10.1038/s41592-021-01101-x · DOI · Paper page
- 10.1038/nbt.3988 · DOI · Paper page
- Zuckerkandl, E. & Pauling, L. in Evolutionary divergence and convergence in proteins (eds Bryson, V. & Vogel, H. J .) Evolving genes and proteins 97–166 (Elsevier, 1965). · DOI · Paper page
- 10.1002/prot.340090107 · DOI
- 10.1016/j.sbi.2005.04.003 · DOI
- 10.1038/nrm2281 · DOI
- 10.1038/nmeth.2340 · DOI · Paper page
- 10.1006/jmbi.1993.1413 · DOI
- 10.1126/science.abj8754 · DOI · Paper page
- 10.1002/prot.26617 · DOI · Paper page
- 10.1101/cshperspect.a041465 · DOI
- Zhang, J. et al. Computing the Human Interactome. bioRxiv 2024.10.01.615885 (2024).
- 10.1016/0022-2836(81)90087-5 · DOI
- 10.1016/0022-2836(82)90398-9 · DOI
- 10.1186/1471-2105-12-221 · DOI
- 10.1093/nar/25.17.3389 · DOI · Paper page
- 10.1186/s12859-019-3019-7 · DOI · Paper page
- 10.1186/s12859-024-05879-3 · DOI
- 10.1186/s12859-016-0946-4 · DOI
- Selvitopi, O. et al. Extreme-scale many-against-many protein similarity search. Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SC ‘22, 1–12 (IEEE Press, 2022). · DOI
- 10.1016/0022-2836(94)90032-9 · DOI
- 10.1186/s12859-024-05965-6 · DOI
- 10.1093/bioinformatics/bty1057 · DOI · Paper page
- 10.1038/s41592-022-01488-1 · DOI · Paper page
- 10.1073/pnas.2016239118 · DOI · Paper page
- 10.1002/prot.26237 · DOI · Paper page
- 10.1038/s41587-023-01773-0 · DOI · Paper page
- 10.1186/s13059-019-1832-y · DOI · Paper page
- 10.1186/s13059-024-03298-4 · DOI · Paper page
- 2023, Poet: A generative model of protein families as sequences-of-sequences, Advances in Neural Information Processing Systems, 36, 77379
- 10.1093/nar/gkq1212 · DOI
- 10.1093/bioinformatics/btl582 · DOI
- 10.1093/nar/27.1.254 · DOI
- 10.1038/s41592-019-0598-1 · DOI · Paper page
- 10.1002/prot.20264 · DOI · Paper page
Metadata
- Authors
- Kallenborn, F., Chacon, A., Hundt, C., Sirelkhatim, H., Didi, K., Cha, S., Dallago, C., Mirdita, M., Schmidt, B., & Steinegger, M.
- Affiliations
- Johannes Gutenberg University Mainz (DE)
- Nvidia (United States) (US)
- University of Oxford (GB)
- Seoul National University (KR)
- Duke University (US)
- Corresponding author
- Dallago, Christian
- Mirdita, Milot
- Schmidt, Bertil
- Steinegger, Martin
- ORCID
- Venue
- Nature Methods
- Publisher
- openRxiv
- Published
- 2024-11-15
- Volume
- 22
- Issue
- 10
- Pages
- 2024-2027
- ISSN
- 1548-7091 (ISSN-L)
- PMC
- PMC12510879
- OpenAlex
- W4414335961
- Cited by
- 72
- References
- 2
- Citations by year
- 2026: 49 · 2025: 23
- FWCI
- 21.34
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature Methods (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Gutenberg Open Science (submittedVersion, cc-by-nd)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Gutenberg Open Science (cc-by)
- Funders
- National Research Foundation (RS-2021-NR061659, RS-2024-00396026, RS-2021-NR056571)
- Deutsche Forschungsgemeinschaft (TRR 319 RMaP, TRR319, TP C01, 439669440, 2020M3A9G7103933)
- National Research Foundation of Korea (2021-R1C1-C102065, 2021-M3A9-I4021220, RS-2021-NR061659, 2020M3‐A9G7‐103933, RS-2024-00396026, RS-2023-00250470, RS-2021-NR056571)
- Johannes Gutenberg-Universität Mainz
- Novo Nordisk
- Novo Nordisk Fonden (NNF24SA0092560)
- Samsung
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Computer Science › Hardware and Architecture › Parallel Computing and Optimization Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- MMseqs2, GPU acceleration, protein homology search, protein sequence databases, protein structure prediction, ColabFold, AlphaFold2, protein structure search, Foldseek
- MeSH terms
- Algorithms, Computer Graphics, Protein Conformation, Proteins, Software, Computational Biology, Databases, Protein
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