ArticleNucleic acids research2017
ECOD: new developments in the evolutionary classification of domains.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Domain classification of archaeal proteomes reveals conserved fold repertoire.PLoS computational biology · 2026Article
- Nature Counts to Three: Universal Mg-Pinch Motif Polarizes the Cleaved Bond in NTP-Processing Enzymes.Journal of the American Chemical Society · 2026Article
- Constraint Decoupled Latent Diffusion for Protein Backmapping.Journal of chemical theory and computation · 2026Article
- Structome-TM: complementing dataset assembly for structural phylogenetics by addressing size-based biases.Bioinformatics advances · 2026Article
- Using evolutionary context to classify difficult protein folds.PLoS computational biology · 2025Article
- Exploration of Comprehensive Structural and Functional Potential of Recombinant Proteins Using Cutting-Edge Bioinformatics Tools.Applied biochemistry and biotechnology · 2025Review
- Article
- Decoding the limits of deep learning in molecular docking for drug discovery.Chemical science · 2025Article
- Gaia: An AI-enabled genomic context-aware platform for protein sequence annotation.Science advances · 2025Article
- Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases.Molecular biology and evolution · 2025Article
- Protein-Peptide Docking with ESMFold Language Model.Journal of chemical theory and computation · 2025Article
- Refinement and curation of homologous groups facilitated by structure prediction.Protein science : a publication of the Protein Society · 2025Article
- Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models.Journal of molecular biology · 2024Article
- BEAN and HABAS: Polyphyletic insertions in the DNA-directed RNA polymerase.Protein science : a publication of the Protein Society · 2024Article
- Graph masked self-distillation learning for prediction of mutation impact on protein-protein interactions.Communications biology · 2024Article
- PMSFF: Improved Protein Binding Residues Prediction through Multi-Scale Sequence-Based Feature Fusion Strategy.Biomolecules · 2024Article
- ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2.PLoS computational biology · 2024Article
- ATLAS: protein flexibility description from atomistic molecular dynamics simulations.Nucleic acids research · 2024Article
- Pan-cancer structurome reveals overrepresentation of beta sandwiches and underrepresentation of alpha helical domains.Scientific reports · 2023Article
- Classification of domains in predicted structures of the human proteome.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
Corrections and comments
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4 authors.
Funding
Abstract
Evolutionary Classification Of protein Domains (ECOD) (http://prodata.swmed.edu/ecod) comprehensively classifies protein with known spatial structures maintained by the Protein Data Bank (PDB) into evolutionary groups of protein domains. ECOD relies on a combination of automatic and manual weekly updates to achieve its high accuracy and coverage with a short update cycle. ECOD classifies the approximately 120 000 depositions of the PDB into more than 500 000 domains in ∼3400 homologous groups. We show the performance of the weekly update pipeline since the release of ECOD, describe improvements to the ECOD website and available search options, and discuss novel structures and homologous groups that have been classified in the recent updates. Finally, we discuss the future directions of ECOD and further improvements planned for the hierarchy and update process.
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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.