ECOD: new developments in the evolutionary classification of domains. Issue Volume 45:Issue D1(2017) (28th November 2016)

• Record Type: Journal Article
• Authors: Schaeffer, R. Dustin; Liao, Yuxing; Cheng, Hua; Grishin, Nick V.
• Is Part Of: Nucleic acids research. Volume 45:Issue D1(2017)
• Page Start: D296
• Page End: D302
• Publication Date: 2016-11-28
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkw1137
• Languages: English
• ISSNs: 0305-1048

Abstract

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.