ArticlePLoS computational biology2024
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Universal and Lineage-Specific Patterns in the Distribution of ECOD Domain Homology Groups Across Superkingdoms.Proteins · 2026Article
- Stable simulations do not guarantee functional engagement: a case study of off-target prediction for Seladelpar and Zanamivir.Journal of computer-aided molecular design · 2026Article
- Domain classification of archaeal proteomes reveals conserved fold repertoire.PLoS computational biology · 2026Article
- Contrastive learning unites sequence and structure in a global representation of protein space.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- T3SS effector and regulator discovery by predicting interacting partners of T3SS chaperones in Pseudomonas aeruginosa.Protein science : a publication of the Protein Society · 2026Article
- AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2.Nature methods · 2026Article
- ECOD: Classification of domains in AFDB Swiss-Prot structure predictions.PLoS computational biology · 2026Article
- DrugDomain 2.0: comprehensive database of protein domains-ligands/drugs interactions across the whole Protein Data Bank.bioRxiv : the preprint server for biology · 2025Article
- Leveraging AI to explore structural contexts of post-translational modifications in drug binding.Journal of cheminformatics · 2025Article
- IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes.PLoS computational biology · 2025Review
- Leveraging AI to Explore Structural Contexts of Post-Translational Modifications in Drug Binding.bioRxiv : the preprint server for biology · 2025Article
- Refinement and curation of homologous groups facilitated by structure prediction.Protein science : a publication of the Protein Society · 2025Article
- A structural atlas of death domain fold proteins reveals their versatile roles in biology and function.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- DrugDomain 2.0: Comprehensive database of protein domains-ligands/drugs interactions across the whole Protein Data Bank.Computational and structural biotechnology journal · 2025Article
- Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models.Journal of molecular biology · 2024Article
- Exploring structural diversity across the protein universe with The Encyclopedia of Domains.Science (New York, N.Y.) · 2024Article
- DrugDomain: The evolutionary context of drugs and small molecules bound to domains.Protein science : a publication of the Protein Society · 2024Article
- Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands.Scientific reports · 2024Article
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6 authors.
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Abstract
Protein structure prediction has now been deployed widely across several different large protein sets. Large-scale domain annotation of these predictions can aid in the development of biological insights. Using our Evolutionary Classification of Protein Domains (ECOD) from experimental structures as a basis for classification, we describe the detection and cataloging of domains from 48 whole proteomes deposited in the AlphaFold Database. On average, we can provide positive classification (either of domains or other identifiable non-domain regions) for 90% of residues in all proteomes. We classified 746,349 domains from 536,808 proteins comprised of over 226,424,000 amino acid residues. We examine the varying populations of homologous groups in both eukaryotes and bacteria. In addition to containing a higher fraction of disordered regions and unassigned domains, eukaryotes show a higher proportion of repeated proteins, both globular and small repeats. We enumerate those highly populated domains that are shared in both eukaryotes and bacteria, such as the Rossmann domains, TIM barrels, and P-loop domains. Additionally, we compare the sampling of homologous groups from this whole proteome set against our stable ECOD reference and discuss groups that have been enriched by structure predictions. Finally, we discuss the implication of these results for protein target selection for future classification strategies for very large protein sets.
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