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CDD/SPARCLE: functional classification of proteins via subfamily domain architectures
Open accessAbstract
NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints. An archive of pre-computed domain annotation is maintained for proteins tracked by NCBI's Entrez database, and live search services are offered as well. CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from external providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families. CDD also supports comparative analyses of protein families via conserved domain architectures, and a recent curation effort focuses on providing functional characterizations of distinct subfamily architectures using SPARCLE: Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.
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- 10.1093/nar/gkv1344 · DOI · Paper page
- Letunic, 2014, SMART: recent updates, new developments, and status in 2015, Nucleic Acids Res., 43, D257, 10.1093/nar/gku949 · DOI
- 10.1093/nar/29.1.22 · DOI · Paper page
- 10.1093/nar/gks1234 · DOI · Paper page
- 10.1093/nar/gkn734 · DOI · Paper page
- 10.1093/nar/gku1221 · DOI · Paper page
- 10.1093/nar/gkh454 · DOI · Paper page
- Finn R. Attwood T. Babbitt P. Bateman A. Bork P. Bridge A. Chang H.-Y. Dosztányi Z. El-Gebali S. Fraser M. . InterPro in 2017: beyond protein family and domain annotations. Nucleic Acids Res. 2017. doi:10.1093/nar/gkw1107. · DOI
- 10.1101/gr.278202 · DOI · Paper page
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Metadata
- Authors
- Marchler-Bauer, A., Bo, Y., Han, L., He, J., Lanczycki, C. J., Lu, S., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Lu, F., Marchler, G. H., Song, J. S., Thanki, N., Wang, Z., Yamashita, R. A., Zhang, D., Zheng, C., Geer, L. Y., & Bryant, S. H.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-11-29
- Volume
- 45
- Issue
- D1
- Pages
- D200-D203
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2559191318
- Cited by
- 2,713
- References
- 0
- FWCI
- 127.00
- Type
- journal article
- Language
- en
- Open access
- gold
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