ArticleNature methods2025
Rapid and sensitive protein complex alignment with Foldseek-Multimer.
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 45 papers.
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Who cites it
45 citing papers in PubMed.
- Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes.bioRxiv : the preprint server for biology · 2026Article
- Reimagining computational macromolecular modeling: AI-driven approaches.Biophysical journal · 2026Review
- Article
- Protein Structure Characters in the Light of Phylogenetic Systematics.Genome biology and evolution · 2026Article
- Structure of the Beat-Side complex reveals their interaction is required for neuromuscular system wiring.Cell reports · 2026Article
- A comparative and exploratory analysis of computational methods for TCR structural prediction and antigen-specific TCR discovery.Briefings in bioinformatics · 2026Article
- Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.Nature communications · 2026Article
- The microbiome regulates host metabolic health and diseases through microbial enzymes.Nature reviews. Gastroenterology & hepatology · 2026Review
- DeepRank-Ab: a scoring function for antibody-antigen complexes based on geometric deep learning.Communications biology · 2026Article
- Structural Assessment of Fibrillated Beta Amyloid to Reveal the Potential Epitopes for Alzheimer's Disease.Cell biochemistry and biophysics · 2026Article
- Improving protein and protein interactions using pseudo-dimers derived from monomeric proteins.Nature communications · 2026Article
- Computational prediction resolves thousands of homooligomeric phage protein structures.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking TCR-pMHC structure prediction: a unified evaluation and CDR3-based functional insights.Briefings in bioinformatics · 2026Article
- AlphaFold-driven discovery of oxysterol-binding protein-related protein-phosphoinositide 3-, 4-, and 5-phosphatase interactions using new generation confidence scores.Protein science : a publication of the Protein Society · 2026Article
- A new family of rolling-circle replication endonucleases widespread in archaeal viruses and plasmids.Nucleic acids research · 2026Article
- Evaluating deep learning based structure prediction methods on antibody-antigen complexes.Bioinformatics (Oxford, England) · 2026Article
- Multi-scale structural similarity embedding search across entire proteomes.Bioinformatics (Oxford, England) · 2026Article
- Microbial dl-Peptidases Enable Predator Defense and Facilitate Structure Elucidation of Complex Natural Products.Journal of the American Chemical Society · 2026Article
- Structural insights into the antibacterial function of the Pseudomonas putida effector Tke5.The EMBO journal · 2026Article
- A fully automated benchmarking suite to compare macromolecular complexes.Nature methods · 2026Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Advances in computational structure prediction will vastly augment the hundreds of thousands of currently available protein complex structures. Translating these into discoveries requires aligning them, which is computationally prohibitive. Foldseek-Multimer computes complex alignments from compatible chain-to-chain alignments, identified by efficiently clustering their superposition vectors. Foldseek-Multimer is 3-4 orders of magnitudes faster than the gold standard, while producing comparable alignments; this allows it to compare billions of complex pairs in 11 h. Foldseek-Multimer is open-source software available at GitHub via https://github.com/steineggerlab/foldseek/ , https://search.foldseek.com/search/ and the BFMD database.
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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.