CDD: a conserved domain database for interactive domain family analysis

By Aron Marchler-Bauer, John B. Anderson, Myra K. Derbyshire, Carol DeWeese-Scott, Noreen R. Gonzales, Marc Gwadz, Luning Hao, Siqian He, David I. Hurwitz, John D. Jackson and 15 more. Nucleic Acids Res., 2006

901 citations recorded by the source corpus.

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 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 . 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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c26bebcd7bb295d52665197f9c842f1d9a78e2b2

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Citations in the corpus

CDD: specific functional annotation with the Conserved Domain Database (2008, background): “CDTree/Cn3D can be set up so that user query sequences can be embedded in previously deﬁned hierarchical classiﬁcations, and so that the assignment of a user query to any particular sub-family can be challenged or conﬁrmed (12).”
Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization (2010, methodology): “The version 2.11 of CDD contains Figure 1.”
A New Method for Predicting the Subcellular Localization of Eukaryotic Proteins with Both Single and Multiple Sites: Euk-mPLoc 2.0 (2010, positive): “Use RPS-BLAST (Reverse PSI-BLAST) program [44] to conduct sequence alignment of the protein sequence with each of the 17,402 domain sequences in the CDD database.”
NetB, a New Toxin That Is Associated with Avian Necrotic Enteritis Caused by Clostridium perfringens (2008, background): “Comparison of NetB against the CDD conserved domain database [22] showed that it contained a leukocidin domain, which is also present in beta-toxin, HlyII and Hla, indicating that NetB belongs to the Leukocidin/Hemolysin family of toxins.”
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. (2008, methodology): “gov/) and the Conserved Domain Database (CDD) (www.ncbi.nlm.nih.gov/Structure/cdd/cdd. shtml; Marchler-Bauer et al. 2007).”
A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation (2008, methodology): “Although most homology search methods are based on local alignment, our previous internal HMMER2 benchmarks and benchmarks of other methods [45] have suggested that glocal alignment is more sensitive and specific when conserved protein domains can be defined a priori (as in protein domain databases ”
Pseudo Amino Acid Composition and its Applications in Bioinformatics, Proteomics and System Biology (2009, methodology): “Based on such a fact, several FunD databases were developed, such as SMART [180], Pfam [181], COG [182], KOG [182], CDD [183].”
Some remarks on protein attribute prediction and pseudo amino acid composition (2010, methodology): “Of these databases, CDD contains the domains imported from COG, Pfam, and SMART, and hence is relatively much more complete (Marchler-Bauer et al., 2007) and was adopted in most of the recent publications (see,e.g.,ChouandShen,2010a,2010c;ShenandChou,2009d).”
Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach (2010, methodology): “Genes were identified phylogenetically as monophyletic ingroups sharing conserved domain architecture using Pfam databases and NCBI’s Conserved Domain Database [77,78] (See Additional File 1 for details).”
Advances and pitfalls of protein structural alignment. (2009, neutral): “The ﬁrst two depend on a manually curated reference alignment (e.g. HOMSTRAD [45], CDD [46,47], Sisyphus [48], BIRC [49]), or classiﬁcation (e.g. SCOP [50] and CATH [51]) as the standard of truth.”
Understanding eukaryotic linear motifs and their role in cell signaling and regulation. (2008, neutral): “Many bioinformatics tools are also available for studies of globular domains, including SMART, Pfam, CDD, SCOP and CATH (6-10).”
Impacts of bioinformatics to medicinal chemistry. (2015, background): “The general form of PseAAC can actually cover all the features hidden in the protein sequence, such as its amino acid composition, K-tuple peptide composition [101-106], functional domain information [107-111], gene ontology [112] information, sequence evolutionary information [113], and all the oth”
Cell-PLoc 2.0: an improved package of web-servers for predicting subcellular localization of proteins in various organisms (2010, background): “0 is closely associated with the GO database [68,112,113] and functional domain database [114], with the continuous development of the GO database and functional domain database, more useful GO numbers and functional domain information will be incorporated into the prediction engine, further strengt”
The Glycosyltransferase Repertoire of the Spikemoss Selaginella moellendorffii and a Comparative Study of Its Cell Wall (2012, positive): “The remaining candidates were then screened by an rpsblast against the conserved domain database CDD [109].”