Searching ECOD for Homologous Domains by Sequence and Structure

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

ECOD is a database of evolutionary domains from structures deposited in the PDB. Domains in ECOD are classified by a mixed manual/automatic method wherein the bulk of newly deposited structures are classified automatically by protein-protein BLAST. Those structures that cannot be classified automatically are referred to manual curators who use a combination of alignment results, functional analysis, and close reading of the literature to generate novel assignments. ECOD differs from other structural domain resources in that it is continually updated, classifying thousands of proteins per week. ECOD recognizes homology as its key organizing concept, rather than structural or sequence similarity alone. Such a classification scheme provides functional information about proteins of interest by placing them in the correct evolutionary context among all proteins of known structure. This unit demonstrates how to access ECOD via the Web and how to search the database by sequence or structure. It also details the distributable data files available for large-scale bioinformatics users.

Original languageEnglish (US)
Article numbere45
JournalCurrent Protocols in Bioinformatics
Volume61
Issue number1
DOIs
StatePublished - Mar 1 2018

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Sequence Homology
Proteins
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Keywords

  • domain classification
  • protein domain
  • sequence search
  • structure search

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry

Cite this

Searching ECOD for Homologous Domains by Sequence and Structure. / Schaeffer, R. Dustin; Liao, Yuxing; Grishin, Nick V.

In: Current Protocols in Bioinformatics, Vol. 61, No. 1, e45, 01.03.2018.

Research output: Contribution to journalArticle

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