ArticleNature methods2025
GPU-accelerated homology search with MMseqs2.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
33 citing papers in PubMed.
- Article
- Graph-based representations in modern protein science.The Biochemical journal · 2026Review
- AI-enabled discovery and biochemical optimization of minibinders targeting cancer cell-surface proteins.Nature communications · 2026Article
- Decoding the allosteric grammar of protein kinases: A dual-stream framework integrating protein language models and energy landscape frustration analysis.Protein science : a publication of the Protein Society · 2026Article
- Genomic insights into the probiotic potential of dairy-associated Saccharomyces cerevisiae WUT3 and WUT151 strains.Functional & integrative genomics · 2026Article
- Substrate scope of ancestral versus modern family-1 glycosidases.Protein science : a publication of the Protein Society · 2026Article
- Noncatalytic surface electrostatic networks tune thermolability in uracil-DNA glycosylase.The Journal of biological chemistry · 2026Article
- Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny.Current protocols · 2026Article
- Accelign: a GPU-based library for accelerating pairwise sequence alignment.BMC bioinformatics · 2026Article
- ANARCII enables alignment-free antigen receptor numbering using a generalised language model.Communications biology · 2026Article
- Repertoire-scale antibody structural prediction informs therapeutic design.Science advances · 2026Article
- A previously unappreciated class of metal-dependent bile salt hydrolases from the human gut microbiome.bioRxiv : the preprint server for biology · 2026Article
- Intracellular and dual-site inhibition of a bitter taste GPCR.Cellular and molecular life sciences : CMLS · 2026Article
- Article
- AlphaFast: High-throughput AlphaFold 3 via GPU-accelerated MSA construction.bioRxiv : the preprint server for biology · 2026Article
- Draft genome of Mn(II)-oxidizing bacteriumMicrobiology resource announcements · 2026Article
- Microbial dl-Peptidases Enable Predator Defense and Facilitate Structure Elucidation of Complex Natural Products.Journal of the American Chemical Society · 2026Article
- Cookbook for plant genome sequences.BMC genomics · 2026Review
- Article
- Protein structure-informed bacteriophage genome annotation with Phold.Nucleic acids research · 2026Article
Corrections and comments
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Authors and funding
10 authors.
Funding
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/ .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.