201:). What is unique about NCBI-curated domains is that they use 3D-structure information to explicitly define domain boundaries, align blocks, amend alignment details, 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. To provide a non-redundant view of the data, CDD clusters similar domain models from various sources into superfamilies.
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sequence/structure/function relationships. To do this, CDD Curators include the following types of information in order to supplement and enrich the traditional multiple sequence alignments that form the foundation of domain models: 3-dimensional structures and conserved core motifs, conserved features/sites, phylogenetic organization, links to electronic literature resources.
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query and retrieval system, crosslinked 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
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Domains can be thought of as distinct functional and/or structural units of a protein. These two classifications coincide rather often, as a matter of fact, and what is found as an independently folding unit of a polypeptide chain also carries specific function. Domains are often identified as
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The goal of the NCBI conserved domain curation project is to provide database users with insights into how patterns of residue conservation and divergence in a family relate to functional properties, and to provide useful links to more detailed information that may help to understand those
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such domains may have been utilized as building blocks, and may have been recombined in different arrangements to modulate protein function. CDD defines conserved domains as recurring units in molecular evolution, the extents of which can be determined by sequence and structure analysis.
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Marchler-Bauer, A.; Zheng, C.; Chitsaz, F.; Derbyshire, M. K.; Geer, L. Y.; Geer, R. C.; Gonzales, N. R.; Gwadz, M.; Hurwitz, D. I.; Lanczycki, C. J.; Lu, F.; Lu, S.; Marchler, G. H.; Song, J. S.; Thanki, N.; Yamashita, R. A.; Zhang, D.; Bryant, S. H. (2012).
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CDD content includes NCBI manually curated domain models and domain models imported from a number of external source databases (
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recurring (sequence or structure) units, which may exist in various contexts. In
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Conserved Domain
Database for the functional annotation of proteins.
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251:"CDD: Conserved domains and protein three-dimensional structure"
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305:. United States National Center for Biotechnology Information.
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219:. United States National Center for Biotechnology Information.
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models and derived database search models, for ancient
303:"Conserved Domains Database (CDD) and Resource Group"
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https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
214:can be queried with novel protein sequences via *
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105:National Center for Biotechnology Information
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49:of all important aspects of the article.
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209:The collection is also part of NCBI's
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122:Marchler-Bauer & al. (2013)
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37:may be too short to adequately
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261:(Database issue): D348–D352.
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217:"the CD-Search service"
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205:Searching the database
224:"the Batch CD-Search"
320:Biological databases
267:10.1093/nar/gks1243
197:, SMART, COG, PRK,
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114:Aron Marchler-Bauer
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86:Description
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232:References
171:Philosophy
221:, or at*
39:summarize
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189:Content
165:domains
140:Website
111:Authors
94:Contact
81:Content
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211:Entrez
135:Access
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151:The
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157:CDD
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Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
