GPU-accelerated homology search with MMseqs2.
Publication
, Journal Article
Kallenborn, F; Chacon, A; Hundt, C; Sirelkhatim, H; Didi, K; Cha, S; Dallago, C; Mirdita, M; Schmidt, B; Steinegger, M
Published in: Nat Methods
October 2025
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/ .
Duke Scholars
Published In
Nat Methods
DOI
EISSN
1548-7105
Publication Date
October 2025
Volume
22
Issue
10
Start / End Page
2024 / 2027
Location
United States
Related Subject Headings
- Software
- Proteins
- Protein Conformation
- Developmental Biology
- Databases, Protein
- Computer Graphics
- Computational Biology
- Algorithms
- 31 Biological sciences
- 11 Medical and Health Sciences
Citation
APA
Chicago
ICMJE
MLA
NLM
Kallenborn, F., Chacon, A., Hundt, C., Sirelkhatim, H., Didi, K., Cha, S., … Steinegger, M. (2025). GPU-accelerated homology search with MMseqs2. Nat Methods, 22(10), 2024–2027. https://doi.org/10.1038/s41592-025-02819-8
Kallenborn, Felix, Alejandro Chacon, Christian Hundt, Hassan Sirelkhatim, Kieran Didi, Sooyoung Cha, Christian Dallago, Milot Mirdita, Bertil Schmidt, and Martin Steinegger. “GPU-accelerated homology search with MMseqs2.” Nat Methods 22, no. 10 (October 2025): 2024–27. https://doi.org/10.1038/s41592-025-02819-8.
Kallenborn F, Chacon A, Hundt C, Sirelkhatim H, Didi K, Cha S, et al. GPU-accelerated homology search with MMseqs2. Nat Methods. 2025 Oct;22(10):2024–7.
Kallenborn, Felix, et al. “GPU-accelerated homology search with MMseqs2.” Nat Methods, vol. 22, no. 10, Oct. 2025, pp. 2024–27. Pubmed, doi:10.1038/s41592-025-02819-8.
Kallenborn F, Chacon A, Hundt C, Sirelkhatim H, Didi K, Cha S, Dallago C, Mirdita M, Schmidt B, Steinegger M. GPU-accelerated homology search with MMseqs2. Nat Methods. 2025 Oct;22(10):2024–2027.
Published In
Nat Methods
DOI
EISSN
1548-7105
Publication Date
October 2025
Volume
22
Issue
10
Start / End Page
2024 / 2027
Location
United States
Related Subject Headings
- Software
- Proteins
- Protein Conformation
- Developmental Biology
- Databases, Protein
- Computer Graphics
- Computational Biology
- Algorithms
- 31 Biological sciences
- 11 Medical and Health Sciences