CDD: a conserved domain database for interactive domain family analysis

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ID: 301883
2006
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Abstract
The conserved domain database (CDD) is part of NCBI's Entrez database system and serves as a primary resource for the annotation of conserved domain footprints on protein sequences in Entrez. Entrez's global query interface can be accessed at Author Webpage and will search CDD and many other databases. Domain annotation for proteins in Entrez has been pre-computed and is readily available in the form of 'Conserved Domain' links. Novel protein sequences can be scanned against CDD using the CD-Search service; this service searches databases of CDD-derived profile models with protein sequence queries using BLAST heuristics, at Author Webpage. Protein query sequences submitted to NCBI's protein BLAST search service are scanned for conserved domain signatures by default. The CDD collection contains models imported from Pfam, SMART and COG, as well as domain models curated at NCBI. NCBI curated models are organized into hierarchies of domains related by common descent. Here we report on the status of the curation effort and present a novel helper application, CDTree, which enables users of the CDD resource to examine curated hierarchies. More importantly, CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies.
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Authors Aron Marchler‐Bauer, J. B. Anderson, Myra K. Derbyshire, C. DeWeese-Scott, Nicole R. Gonzales, Marya Gwadz, Luning Hao, Siqian He, David I. Hurwitz, John David Jackson, Ke Zhang, D. Krylov, Christopher J. Lanczycki, C Liebert, C. Liu, Feiteng Lu, Shuo Lu, Gabriele H. Marchler, Michael Mullokandov, James S. Song, Narmada Thanki, Roxanne A. Yamashita, JuanJuan Yin, Dapeng Zhang, Stephen H. Bryant
Journal Nucleic Acids Research
Year 2006
DOI
10.1093/nar/gkl951
URL
https://doi.org/10.1093/nar/gkl951
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