Searching ECOD for Homologous Domains by Sequence and Structure. Issue 1 (9th April 2018)

• Record Type: Journal Article
• Authors: Schaeffer, R. Dustin; Liao, Yuxing; Grishin, Nick V.
• Editors: Baxevanis, Andreas D.; Petsko, Gregory A.; Stein, Lincoln D.; Stormo, Gary D.
• Is Part Of: Current protocols in bioinformatics. Volume 61:Issue 1(2018)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2018-04-09
• Subjects: domain classification -- protein domain -- sequence search -- structure search; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/cpbi.45
• Languages: English
• ISSNs: 1934-3396

Abstract

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. © 2018 by John Wiley & Sons, Inc.