ArticleBioinformatics (Oxford, England)2024
Protein structure alignment by Reseek improves sensitivity to remote homologs.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Evolving strategies for virus discovery.Microbial genomics · 2026Review
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- Exploring the structural lexicon of the Proteome via Metric Geometry.PLoS computational biology · 2026Article
- Much ado about nothing: modeling amino acid replacement with predicted protein structures.Bioinformatics (Oxford, England) · 2026Article
- A H3K27me3 reader complex couples H3K27me3 accumulation to nascent transcription of transposable elements in Paramecium.Genome biology · 2026Article
- Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.Nucleic acids research · 2026Article
- Exploring the protein universe with distant similarity detection methods.Protein science : a publication of the Protein Society · 2026Review
- Exploring the Structural Lexicon of the Proteome via Metric Geometry.bioRxiv : the preprint server for biology · 2025Article
- A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.bioRxiv : the preprint server for biology · 2025Article
- Antiviral reverse transcriptases reveal the evolutionary origin of telomerase.bioRxiv : the preprint server for biology · 2025Article
- Recent advances in the inference of deep viral evolutionary history.Journal of virology · 2025Review
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- 3-D substructure search by transitive closure in AlphaFold database.Protein science : a publication of the Protein Society · 2025Article
- Integrating Sequence- and Structure-Based Similarity Metrics for the Demarcation of Multiple Viral Taxonomic Levels.Viruses · 2025Article
- Tandem Repeats Provide Evidence for Convergent Evolution to Similar Protein Structures.Genome biology and evolution · 2025Article
- Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems.Nucleic acids research · 2025Article
- Stunning Intricacies of RNA Editing Complexes RECC, RESC, and REH2C: Functional Organization, Developmental Regulation, and Evolutionary History in Kinetoplastid Protists.Wiley interdisciplinary reviews. RNAReview
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Abstract
motivationRecent breakthroughs in protein fold prediction from amino acid sequences have unleashed a deluge of new structures, presenting new opportunities and challenges to bioinformatics.
resultsReseek is a novel protein structure alignment algorithm based on sequence alignment where each residue in the protein backbone is represented by a letter in a "mega-alphabet" of 85 899 345 920 (∼1011) distinct states. Reseek achieves substantially improved sensitivity to remote homologs compared to state-of-the-art methods including DALI, TMalign, and Foldseek, with comparable speed to Foldseek, the fastest previous method. Scaling to large databases of AI-predicted folds is analyzed. Foldseek E-values are shown to be under-estimated by several orders of magnitude, while Reseek E-values are in good agreement with measured error rates. AVAILABILITY AND IMPLEMENTATION: https://github.com/rcedgar/reseek.
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