ArticleScience (New York, N.Y.)2024
Exploring structural diversity across the protein universe with The Encyclopedia of Domains.
Article in Science (New York, N.Y.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers, 1 of them a synthesis that pooled it.
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Who cites it
85 citing papers in PubMed, 1 synthesis or guideline pooled it.
- (Re)defining the human chromatome: an integrated meta-analysis of localization, function, abundance, physical properties, and domain composition of chromatin proteins.Nucleic acids research · 2026Pooled it
- High-throughput analyses ofGut microbes · 2026Article
- Mapping the functional dark proteome in cancer.Nature reviews. Cancer · 2026Review
- Molecular mechanism of complement interference by Streptococcus pyogenes nuclease A.Communications biology · 2026Article
- Latent generative search unlocks de novo design of untapped biomolecular interactions at scale.bioRxiv : the preprint server for biology · 2026Article
- Systematic discovery of circular permutations across the protein universe using CIRPIN.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Unsupervised discovery of functional sequence patterns from protein language model with MotifAE.Nature communications · 2026Article
- Investigating enzyme function by geometric matching of catalytic motifs.Protein science : a publication of the Protein Society · 2026Article
- pSB3, a member of the 2-micron family of plasmids, replicates and is efficiently partitioned in multiple budding yeast species.G3 (Bethesda, Md.) · 2026Article
- ECLIPSE: exploring the dark proteome of ESKAPE pathogens through the sequence similarity network of the Protein Universe Atlas.Bioinformatics (Oxford, England) · 2026Article
- Variant characterization in the intrinsically disordered human proteome.Nature structural & molecular biology · 2026Article
- Benchmarking protein sequence and structure search methods for remote homology detection.Genome biology · 2026Article
- FoldDelay web server: an online tool to quantify translation-driven delays in protein native contact formation.Nucleic acids research · 2026Article
- AlphaFind v2: similarity search in AlphaFold DB and TED domains across structural contexts.Nucleic acids research · 2026Article
- TEDLH: domain HMMs for sensitive detection of remote homologues.Bioinformatics (Oxford, England) · 2026Article
- Where next for structural bioinformatics?PLoS biology · 2026Article
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- Structural basis of NMI-IFP35 domains and swapping phenomenon in IFP35-NID.Journal of structural biology: X · 2026Article
- Exploring the structural lexicon of the Proteome via Metric Geometry.PLoS computational biology · 2026Article
- Evolutionary analysis of transcription elongation factors reveals conserved and lineage-specific regulatory domains.PLoS biology · 2026Article
25 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted protein structures composed of domains, which are independently folding units found in multiple structural and functional contexts. Identifying domains can enable many functional and evolutionary analyses but has remained challenging because of the sheer scale of the data. Using deep learning methods, we have detected and classified every domain in the AFDB, producing The Encyclopedia of Domains. We detected nearly 365 million domains, over 100 million more than can be found by sequence methods, covering more than 1 million taxa. Reassuringly, 77% of the nonredundant domains are similar to known superfamilies, greatly expanding representation of their domain space. We uncovered more than 10,000 new structural interactions between superfamilies and thousands of new folds across the fold space continuum.
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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.