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CDD: NCBI's conserved domain database
Open accessAbstract
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.
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Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Research works printed but not linked: 12
- Finn, 2014, Pfam: the protein families database, Nucleic Acids Res., 42, D222, 10.1093/nar/gkt1223 · DOI · Paper page
- Letunic, 2014, SMART: recent updates, new developments, and status in 2015, Nucleic Acids Res.
- Tatusov, 2001, The COG database: new developments in phylogenetic classification of proteins from complete genomes, Nucleic Acids Res., 29, 22, 10.1093/nar/29.1.22 · DOI
- Haft, 2013, TIGRFAMs and Genome Properties in 2013, Nucleic Acids Res., 41, D387, 10.1093/nar/gks1234 · DOI
- Klimke, 2009, The National Center for Biotechnology Information's Protein Clusters Database, Nucleic Acids Res., 37, D216, 10.1093/nar/gkn734 · DOI
- Marchler-Bauer, 2003, CDD: a curated Entrez database of conserved domain alignments, Nucleic Acids Res., 31, D383, 10.1093/nar/gkg087 · DOI
- Schäffer, 2001, Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements, Nucleic Acids Res., 29, 2994, 10.1093/nar/29.14.2994 · DOI
- Marchler-Bauer, 2005, CD-Search: protein domain annotations on the fly, Nucleic Acids Res., 32, W327, 10.1093/nar/gkh454 · DOI
- Geer, 2002, CDART: protein homology by domain architecture, Genome Res., 12, 1619, 10.1101/gr.278202 · DOI · Paper page
- Gray, 2009, Novel beta-propeller of the BTB-Kelch protein Krp1 provides a binding site for Lasp-1 that is necessary for pseudopodial extension, J. Biol. Chem., 284, 30489, 10.1074/jbc.M109.023259 · DOI
- Madej, 2014, MMDB and VAST+: tracking structural similarities between macromolecular complexes, Nucleic Acids Res., 42, D297, 10.1093/nar/gkt1208 · DOI
- Derbyshire, 2012, Annotation of functional sites with the Conserved Domain Database, Database, 10.1093/database/bar058 · DOI
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Metadata
- Authors
- Marchler-Bauer, A., Derbyshire, M. K., Gonzales, N. R., Lu, S., Chitsaz, F., Geer, L. Y., Geer, R. C., He, J., Gwadz, M., Hurwitz, D. I., Lanczycki, C. J., Lu, F., Marchler, G. H., Song, J. S., Thanki, N., Wang, Z., Yamashita, R. A., Zhang, D., Zheng, C., & Bryant, S. H.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-11-20
- Volume
- 43
- Issue
- D1
- Pages
- D222-D226
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2153544371
- Cited by
- 3,433
- References
- 1
- FWCI
- 134.46
- Type
- journal article
- Language
- en
- Open access
- gold
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- Marchler-Bauer, A., Derbyshire, M. K., Gonzales, N. R., Lu, S., Chitsaz, F., Geer, L. Y., Geer, R. C., He, J., Gwadz, M., Hurwitz, D. I., Lanczycki, C. J., Lu, F., Marchler, G. H., Song, J. S., Thanki, N., Wang, Z., Yamashita, R. A., Zhang, D., Zheng, C., & Bryant, S. H. (2015). CDD: NCBI's conserved domain database. Nucleic Acids Research. https://doi.org/10.1093/nar/gku1221
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