Searching ECOD for Homologous Domains by Sequence and Structure

Curr Protoc Bioinformatics. 2018 Mar;61(1):e45. doi: 10.1002/cpbi.45.


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.

Keywords: domain classification; protein domain; sequence search; structure search.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Computational Biology / methods*
  • Databases, Protein*
  • Protein Domains*
  • Proteins / chemistry*
  • Sequence Alignment
  • Sequence Homology, Amino Acid*
  • Structural Homology, Protein*


  • Proteins