Classification of proteins with shared motifs and internal repeats in the ECOD database

Protein Science : a Publication of the Protein Society
R Dustin SchaefferNick V Grishin

Abstract

Proteins and their domains evolve by a set of events commonly including the duplication and divergence of small motifs. The presence of short repetitive regions in domains has generally constituted a difficult case for structural domain classifications and their hierarchies. We developed the Evolutionary Classification Of protein Domains (ECOD) in part to implement a new schema for the classification of these types of proteins. Here we document the ways in which ECOD classifies proteins with small internal repeats, widespread functional motifs, and assemblies of small domain-like fragments in its evolutionary schema. We illustrate the ways in which the structural genomics project impacted the classification and characterization of new structural domains and sequence families over the decade.

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Citations

Dec 3, 2016·Nucleic Acids Research·R Dustin SchaefferNick V Grishin
Apr 17, 2018·Bioinformatics·Yuxing LiaoNick V Grishin
Jun 23, 2019·BMC Molecular and Cell Biology·R Dustin SchaefferNick Grishin
Jun 17, 2020·Proteins·Archana S BhatNick V Grishin
Feb 13, 2020·BMC Evolutionary Biology·David E NorthoverDavid A Liberles
Oct 3, 2020·Protein Science : a Publication of the Protein Society·Bram MylemansArnout R D Voet
Jan 28, 2021·Molecular Biology and Evolution·Rachel KolodnyNir Ben-Tal
Jun 3, 2021·International Journal of Molecular Sciences·Anastasia D GaziVasiliki E Fadouloglou

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