ECOD: new developments in the evolutionary classification of domains

By R. D. Schaeffer, Yuxing Liao, Hua Cheng, Nick V. Grishin. 2016

90 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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Citations in the corpus

The Pfam protein families database in 2019 (2018, background): “To incorporate the EUFs, we performed a search of the corresponding profile HMMs from ECOD against pfam-seq .”
Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints (2018, methodology): “There are no structures in the DMPfold training set in the same ECOD [21] T-group as these domains.”
Dali server: structural unification of protein families (2022, unknown): “However, the sheer volume of the AlphaFold Database is a practical obstacle and we are not aware of support for AF-DB in other traditional structure database search servers (29– 31) or in structural classifications (32–34).”
Improving peptide-protein docking with AlphaFold-Multimer using forced sampling (2021, methodology): “After selecting one complex representative per ECOD (Schaeffer et al., 2017) family, the ﬁ nal redundancy reduced set consisted of 112 peptide-protein complexes.”
Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation (2025, unknown): “Tools like ProtTrek ( 12 ), pLM-BLAST ( 13 ), and PLMSearch ( 14 ) use protein language models for remote homology detection ( 15 ) by comparing against databases like Swiss-Prot ( 16 ) and ECOD ( 17 ).”