CDD: a Conserved Domain Database for protein classification

By Aron Marchler-Bauer, John B. Anderson, Praveen F. Cherukuri, Carol DeWeese-Scott, Lewis Y. Geer, Marc Gwadz, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke and 14 more. Nucleic Acids Res., 2004

1,208 citations recorded by the source corpus.

The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein–protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.

Subfields: Molecular Biology

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Citations in the corpus

CDD: specific functional annotation with the Conserved Domain Database (2008, methodology): “This mapping of superfamily ‘generic’ sites is made possible by NCBI-curated domain hierarchies following a strictly validated alignment model that permits such computation and has been discussed previously ( 11 ).”
PubChem as a public resource for drug discovery (2010, methodology): “…potential functions of these bioassay targets, we performed sequence similarity search against the annotated functional domains in the NCBI Conserved Domain Database (CDD, http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) [12] by using the reverse position specific BLAST (RPS-Blast) tool [13].”
Expanded microbial genome coverage and improved protein family annotation in the COG database (2014, methodology): “In 2003, COGs have been incorporated into the NCBI’s Conserved Domain Database (CDD; (2,3)).”
A novel method to compare protein structures using local descriptors (2011, methodology): “When tested on a relatively simple Conserved Domain Database [46], current automated techniques usually misalign residue pairs that are more than (a) (b)”
ARDB—Antibiotic Resistance Genes Database (2008, methodology): “In addition to BLAST we also provide an RPSBLAST (19) interface relying on Position Specific Scoring Matrix (PSSM) created from sequences associated with each resistance type, using an approach similar to the NCBI Conserved Domain Database (20).”
CDD: a conserved domain database for interactive domain family analysis (2006, methodology): “To this end, the CDD (1) provides a strategy toward a more accurate assessment of such neighbor relationships, similar to approaches termed ‘phylogenomic inference’ (2).”
Database resources of the National Center for Biotechnology Information: update (2004, methodology): “The structures in the MMDB are linked to sequences in Entrez and to the Conserved Domain Database ( 6 ).”
Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation (2008, background): “The PGAAP combines Hidden Markov Model (HMM)- based gene prediction methods with a sequence similarity-based approach which combines comparison of the predicted gene products to the nonredundant protein database, Entrez Protein Clusters (Wheeler et al., 2008), the Conserved Domain Database (Marchler”
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline (2007, background): “The potential 50 UTRs of genes classified in the Conserved Domain Database (18) version 2.”