CDD: specific functional annotation with the Conserved Domain Database.

Published

Journal Article

NCBI's Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. The collection can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml, and is also part of NCBI's Entrez query and retrieval system, cross-linked to numerous other resources. CDD provides annotation of domain footprints and conserved functional sites on protein sequences. Precalculated domain annotation can be retrieved for protein sequences tracked in NCBI's Entrez system, and CDD's collection of models can be queried with novel protein sequences via the CD-Search service at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. Starting with the latest version of CDD, v2.14, information from redundant and homologous domain models is summarized at a superfamily level, and domain annotation on proteins is flagged as either 'specific' (identifying molecular function with high confidence) or as 'non-specific' (identifying superfamily membership only).

Full Text

Cited Authors

  • Marchler-Bauer, A; Anderson, JB; Chitsaz, F; Derbyshire, MK; DeWeese-Scott, C; Fong, JH; Geer, LY; Geer, RC; Gonzales, NR; Gwadz, M; He, S; Hurwitz, DI; Jackson, JD; Ke, Z; Lanczycki, CJ; Liebert, CA; Liu, C; Lu, F; Lu, S; Marchler, GH; Mullokandov, M; Song, JS; Tasneem, A; Thanki, N; Yamashita, RA; Zhang, D; Zhang, N; Bryant, SH

Published Date

  • January 2009

Published In

Volume / Issue

  • 37 / Database issue

Start / End Page

  • D205 - D210

PubMed ID

  • 18984618

Pubmed Central ID

  • 18984618

Electronic International Standard Serial Number (EISSN)

  • 1362-4962

Digital Object Identifier (DOI)

  • 10.1093/nar/gkn845

Language

  • eng

Conference Location

  • England