ArticlePLoS computational biology2014
ECOD: an evolutionary classification of protein domains.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 263 papers.
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Who cites it
263 citing papers in PubMed.
- Article
- Universal and Lineage-Specific Patterns in the Distribution of ECOD Domain Homology Groups Across Superkingdoms.Proteins · 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
- Domain classification of archaeal proteomes reveals conserved fold repertoire.PLoS computational biology · 2026Article
- Conserved protein folds underpin the diversification of secreted proteins in a fungal pathogen.BMC microbiology · 2026Article
- The history of enzyme evolution embedded in metabolism.Proceedings of the National Academy of Sciences of the United States of America · 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
- Strategic Template Filtering Accelerates Fragment-Based Peptide Docking.Journal of chemical information and modeling · 2026Article
- An adaptor for feedback regulation of heme biosynthesis by a mitochondrial protease.Science (New York, N.Y.) · 2026Article
- Nature Counts to Three: Universal Mg-Pinch Motif Polarizes the Cleaved Bond in NTP-Processing Enzymes.Journal of the American Chemical Society · 2026Article
- TEDLH: domain HMMs for sensitive detection of remote homologues.Bioinformatics (Oxford, England) · 2026Article
- pLM-Repeat: Exploiting the sequence representations of protein language models for sensitive repeat detection.Protein science : a publication of the Protein Society · 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
- Family-level specialization in protein domain insertion architectures.Protein science : a publication of the Protein Society · 2026Article
- Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily.Nature communications · 2026Article
- Enhancing mutation impact prediction in protein-protein interactions through interpretable graph-based multi-level feature interactions.Bioinformatics (Oxford, England) · 2026Article
- Capsular specificity in temperate phages of Klebsiella pneumoniae is driven by diverse receptor-binding enzymes.PLoS biology · 2026Article
- Clustering the protein universe of life using DIAMOND DeepClust.Nature methods · 2026Article
- Multivalent weak contacts shape chaperone-nascent protein interactions.bioRxiv : the preprint server for biology · 2026Article
- AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2.Nature methods · 2026Article
203 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or "fold"). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies.
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