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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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Cites
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Svartström, O., Alneberg, J., Terrapon, N., Lombard, V., de Bruijn, I., Malmsten, J., Dalin, A.-M., EL Muller, E., Shah, P., Wilmes, P., et al. (2017) · The ISME Journal · doi:10.1038/ismej.2017.108 · Cited by 161
Bouchard, D. S., Seridan, B., Saraoui, T., Rault, L., Germon, P., Gonzalez-Moreno, C., Nader-Macias, F. M. E., Baud, D., François, P., Chuat, V., et al. (2015) · PLOS ONE · doi:10.1371/journal.pone.0144831 · Cited by 144
FIGL1 and its novel partner FLIP form a conserved complex that regulates homologous recombination
Fernandes, J. B., Duhamel, M., Seguéla-Arnaud, M., Froger, N., Girard, C., Choinard, S., Solier, V., De Winne, N., De Jaeger, G., Gevaert, K., et al. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007317 · Cited by 116
“AtFLIP and hFLIP sharing only 12% sequence identity), but they all harbor a specific DUF4487 domain (Domain of Unknown Function) [39], further supporting their orthology.”
BackgroundChang, Y.-C., Hu, Z., Rachlin, J., Anton, B. P., Kasif, S., Roberts, R. J., & Steffen, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1324 · Cited by 56
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Cheng, W., Doering, J. A., LaLone, C., & Ng, C. (2021) · Toxicological Sciences · doi:10.1093/toxsci/kfab004 · Cited by 49
Kolondra, A., Labedzka-Dmoch, K., Wenda, J. M., Drzewicka, K., & Golik, P. (2015) · BMC Genomics · doi:10.1186/s12864-015-2078-z · Cited by 33
“Analysis using the NCBI conserved domain database (CDD, [115]) revealed that all four putative proteins encoded by the introns of the COX1 gene contain the LAGLIDADG endonuclease domain [116], that is found in proteins exhibiting RNA maturase (splicing), DNA endonuclease (homing), or both maturase and endonuclease act…”
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Mehra, Y., & Viswanathan, P. (2021) · PLOS ONE · doi:10.1371/journal.pone.0260116 · Cited by 27
The Birth-and-Death Evolution of Cytochrome P450 Genes in Bees
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Scoring alignments by embedding vector similarity
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ECOD: Classification of domains in AFDB Swiss-Prot structure predictions
Schaeffer, R. D., Zhang, J., Cong, Q., & Grishin, N. V. (2026) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1013431 · Cited by 2
“While resources like InterPro already excel at integrating numerous domain classifications - Pfam [9], Gene3D [27], PROSITE [28], CDD [10,29] - and include some structural resources, they primarily rely on sequence-based approaches.”
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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