CDD: a Conserved Domain Database for the functional annotation of proteins

By Aron Marchler-Bauer, Shennan Lu, John B. Anderson, Farideh Chitsaz, Myra K. Derbyshire, Carol DeWeese-Scott, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales and 17 more. 2010

3,210 citations recorded by the source corpus.

NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As CDD also imports domain family models from a variety of external sources, it is a partially redundant collection. To simplify protein annotation, redundant models and models describing homologous families are clustered into superfamilies. By default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership. Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein queries. CDD can be accessed via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

Subfields: Molecular Biology, Pharmacology

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Citations in the corpus

ECOD: An Evolutionary Classification of Protein Domains (2014, background): “hensive sequence-based classifications such as Pfam [1] and CDD [2] are among the most popular protein annotation tools.”
CDD: conserved domains and protein three-dimensional structure (2012, methodology): “For detailed explanations of the tools and data provided by CDD, we direct the reader to the on-line documentation and earlier manuscripts (9).”
TIGRFAMs and Genome Properties in 2013 (2012, positive): “A CDD entry built from a TIGRFAMs model, e.g. CDD:188483 derived from TIGR03968 (‘mycofactocin system transcriptional regula-tor’), may attach a region feature to many proteins that we were careful to exclude when our model was constructed.”
Cyclic di-GMP: the First 25 Years of a Universal Bacterial Second Messenger (2013, background): “In the GGDEF domain, the active site includes the catalytic Asp/Glu residue surrounded on each side by two strongly conserved residues, which together form the eponymous 79GG(D/E)EF83 sequence motif in the A site (113) (residue numbering is from the GGDEF domain model in the NCBI’s Conserved Domain ”
Assessment of template based protein structure predictions in CASP9 (2011, background): “2–6 However, many applications require atomic models of high resolution, for example, for designing and interpreting amino acid mutations or studying molecular mechanisms such as ligand binding, transport phenomena, or catalytic processes.”
Searching ECOD for homologous domains by sequence and structure (2018, neutral): “If close homologs are not found, searches could be moved to more sensitive sequence proﬁle techniques such as HHsearch or CDD (Marchler-Bauer et al., 2011; Sod-ing, 2005).”
Domain enhanced lookup time accelerated BLAST (2012, methodology): “We computed for each method the fraction of TPs with E -value up to each method-specific threshold, with query and subject sequences matching significantly to the same CD, the same CDD superfamily [26], different CDD superfamilies, or with at least one sequence matching no CD (see Methods ).”
Database resources of the National Center for Biotechnology Information (2011, methodology): “NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map V”
Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. (2014, methodology): “The CDD (Marchler-Bauer et al. 2011) and clusters of orthologous gene profile databases are searched using RPSBLAST (Altschul et al.”
Systematic discovery of anti-phage defense systems in the microbial pan-genome (2018, methodology): “A. Marchler-Bauer et al., CDD: A conserved domain database for the functional annotation of proteins.”
Protein sequence comparison and fold recognition: progress and good-practice benchmarking. (2011, background): “[5–7].”
In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing (2014, background): “In particular, the replicase proteins showing the pfam02387 or pfam01051 conserved domains were assigned to the FII and FIB groups, respectively (31).”
Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems (2015, positive): “against the Conserved Domains database (78).”
Inaugural Article: The protein expression landscape of the Arabidopsis root (2012, neutral): “At1g01910 encodes a protein with anion-transporting ATPase and RAS GTPase domains (48), suggesting a unique role in root hair morphogenesis.”