CDD: NCBI's conserved domain database

Abstract

NCBI's CDD, the Conserved Domain Database, enters its 15(th) year as a public resource for the annotation of proteins with the location of conserved domain footprints. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD. We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. We also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. CDD can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

Keywords

AnnotationDomain (mathematical analysis)BiologyPublic domainProtein domainConsistency (knowledge bases)Computational biologyDatabaseProtein structure databaseSequence alignmentConserved sequenceSequence (biology)Computer scienceInformation retrievalSequence databaseBioinformaticsGeneticsPeptide sequenceGeneArtificial intelligence

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Publication Info

Year: 2014
Type: article
Volume: 43
Issue: D1
Pages: D222-D226
Citations: 3444
Access: Closed

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APA Style

                            
                                
                                    Aron Marchler‐Bauer, 
                                
                                    Myra K. Derbyshire, 
                                
                                    Noreen R. Gonzales
                                
                                et al.
                            
                            (2014). 
                            CDD: NCBI's conserved domain database. 
                            Nucleic Acids Research
                            , 43
                            (D1)
                            , D222-D226.
                            https://doi.org/10.1093/nar/gku1221
                        

Identifiers

DOI: 10.1093/nar/gku1221