CDD: specific functional annotation with the Conserved Domain Database

Aron Marchler‐Bauer(National Center for Biotechnology Information), James B. Anderson(National Center for Biotechnology Information), Farideh Chitsaz(National Institutes of Health), Myra K. Derbyshire(National Center for Biotechnology Information), C. DeWeese-Scott(National Center for Biotechnology Information), Jessica H. Fong(National Institutes of Health), Lewis Y. Geer(National Center for Biotechnology Information), Renata C. Geer(National Center for Biotechnology Information), Nicole R. Gonzales(National Center for Biotechnology Information), Marya Gwadz(National Institutes of Health), Susu He(National Institutes of Health), David I. Hurwitz(National Institutes of Health), John D. Jackson(National Institutes of Health), Zhaoxi Ke(National Institutes of Health), Christopher J. Lanczycki(National Center for Biotechnology Information), C Liebert(National Institutes of Health), C. Liu(National Institutes of Health), Fuping Lu(National Institutes of Health), Shuo Lu(National Center for Biotechnology Information), Gabriele H. Marchler(National Center for Biotechnology Information), Michael Mullokandov(National Center for Biotechnology Information), James S. Song(National Institutes of Health), A. Tasneem(National Center for Biotechnology Information), Narmada Thanki(National Center for Biotechnology Information), Roxanne A. Yamashita(National Institutes of Health), Dapeng Zhang(National Institutes of Health), Nong Zhang(National Institutes of Health), Stephen H. Bryant(National Center for Biotechnology Information)
Nucleic Acids Research
November 4, 2008
10.1093/nar/gkn845
Cited by 1,065Open Access
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Abstract

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).

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