ECOD: New developments in the evolutionary classification of domains

R. Dustin Schaeffer, Yuxing Liao, Hua Cheng, Nick V. Grishin

Research output: Contribution to journalArticle

17 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)D296-D302
JournalNucleic Acids Research
Volume45
Issue numberD1
DOIs
StatePublished - Jan 1 2017

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Databases
Proteins
Protein Domains
Direction compound

ASJC Scopus subject areas

  • Genetics

Cite this

ECOD : New developments in the evolutionary classification of domains. / Dustin Schaeffer, R.; Liao, Yuxing; Cheng, Hua; Grishin, Nick V.

In: Nucleic Acids Research, Vol. 45, No. D1, 01.01.2017, p. D296-D302.

Research output: Contribution to journalArticle

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