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

R. Dustin Schaeffer, Lisa N. Kinch, Yuxing Liao, Nick V. Grishin

Research output: Contribution to journalReview article

8 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1188-1203
Number of pages16
JournalProtein Science
DOIs
StatePublished - Jul 1 2016

Fingerprint

Protein Databases
Proteins
Nucleic Acid Repetitive Sequences
Genomics
Protein Domains

Keywords

  • internal
  • protein classification
  • protein motifs
  • repeats
  • structural bioinformatics
  • structural genomics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Classification of proteins with shared motifs and internal repeats in the ECOD database. / Schaeffer, R. Dustin; Kinch, Lisa N.; Liao, Yuxing; Grishin, Nick V.

In: Protein Science, 01.07.2016, p. 1188-1203.

Research output: Contribution to journalReview article

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