CDD: specific functional annotation with the Conserved Domain Database

By Aron Marchler-Bauer, John B. Anderson, Farideh Chitsaz, Myra K. Derbyshire, Carol DeWeese-Scott, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz and 18 more. Nucleic Acids Res., 2008

1,156 citations recorded by the source corpus.

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).

Subfields: Molecular Biology

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Citations in the corpus

An overview of the PubChem BioAssay resource (2009, background): “Additionally, protein targets are linked to the curated NCBI Conserved Domain Database (CDD) (19) (http://www. ncbi.nlm.nih.gov/cdd) and to three-dimensional structures of closely related proteins contained in the NCBI Molecular Modeling Database (MMDB) (20) (http://www.ncbi.nlm.nih.gov/structure).”
dbCAN: a web resource for automated carbohydrate-active enzyme annotation (2012, methodology): “This is clearly becoming a bottleneck and is not consistent with the way the other popular protein domain/ family databases such Pfam (11), InterPro (12) and CDD (13) handle the annotation needs, which all provide data and automated services through their websites.”
CDD: a Conserved Domain Database for the functional annotation of proteins (2010, background): “Various aspects of CDD have been highlighted in earlier manuscripts (6); here we”
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”
Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea (2011, methodology): “The first criterium was based on identification of functional domains (e.g. InterProScan, CDD) or topology/targeting domains (e.g. Sig-nalP, TargetP, TMHMM) (see M7).”
FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end–directed vesicle transport (2010, methodology): “Analyses using the Conserved Domain Database (Marchler-Bauer et al., 2009) and COILS web server (Lupas et al.”
Classification, Naming and Evolutionary History of Glycosyltransferases from Sequenced Green and Red Algal Genomes (2013, background): “Hit sequences were rpsblasted against the conserved domain database (CDD; [14].”
Database resources of the National Center for Biotechnology Information (2009, methodology): “The NCBI MMDB (46) contains experimentally determined coordinate sets from the Protein Data Bank (47), augmented with domain annotations and links to relevant literature, protein and nucleotide sequences, chemicals (PDB heterogens) and conserved domains in CDD (48) as well as structural neighbors co”
Database resources of the National Center for Biotechnology Information (2006, methodology): “The CDD (61) contains >46000 PSI-BLAST-derived Position Specific Score Matrices representing domains taken from the Simple Modular Architecture Research Tool (62), Pfam (63), TIGRFAM (64) and from domain alignments derived from COGs and Protein Clusters.”
Database resources of the National Center for Biotechnology Information (2014, methodology): “In addition, CDD includes superfamily records that contain sets of CDs from one or more source databases that generate overlapping annotation on the same protein sequences.”