CDD: conserved domains and protein three-dimensional structure

Nucleic Acids Res. 2013 Jan;41(Database issue):D348-52. doi: 10.1093/nar/gks1243. Epub 2012 Nov 28.


CDD, the Conserved Domain Database, is part of NCBI's Entrez query and retrieval system and is also accessible via CDD provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints. Pre-computed annotation is available via Entrez, and interactive search services accept single protein or nucleotide queries, as well as batch submissions of protein query sequences, utilizing RPS-BLAST to rapidly identify putative matches. CDD incorporates several protein domain and full-length protein model collections, and maintains an active curation effort that aims at providing fine grained classifications for major and well-characterized protein domain families, as supported by available protein three-dimensional (3D) structure and the published literature. To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Amino Acid Sequence
  • Conserved Sequence
  • Databases, Protein*
  • Internet
  • Models, Molecular
  • Molecular Sequence Annotation
  • Protein Conformation*
  • Protein Structure, Tertiary*
  • Proteins / chemistry
  • Proteins / classification
  • Proteins / genetics
  • Sequence Analysis, Protein


  • Proteins