Conserved Domains and Protein Classification
 
 
 
 
Citing the Resources
 
 
  Conserved Domain Database (CDD)
  Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Zhang D, Bryant SH. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. 2013 Jan 1;41(D1):D348-52. Epub 2012 Nov 28. [PubMed PMID: 23197659] [Full Text]
   
  CD-Search & Batch CD-Search
  Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31. [PubMed PMID: 15215404] [Full Text]
(Note: The NAR 2011 article on the Conserved Domain Database, listed under "Additional Journal Articles," below, discusses Batch CD-Search. Please cite that paper if using the Batch CD-Search tool.)
   
  CDTree
  Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 2007 Jan;35(Database issue):D237-40. Epub 2006 Nov 29. [PubMed PMID: 17135202] [Full Text]
   
  Conserved Domain Architecture Retrieval Tool (CDART)
  Geer LY, Domrachev M, Lipman DJ, Bryant SH. CDART: protein homology by domain architecture. Genome Res. 2002 Oct;12(10):1619-23. [PubMed PMID: 12368255] [Full Text]
   
 
 
 
Additional Journal Articles
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  Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH. CDD: NCBI's conserved domain database. Nucleic Acids Res. 2014 Nov 20. pii: gku1221. [Epub ahead of print] [PubMed PMID: 21109532] [Full Text]
  Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE. cddApp: A Cytoscape App for Accessing the NCBI Conserved Domain Database. Bioinformatics 2014 Sep 10. pii: btu605. [Epub ahead of print] [PubMed PMID: 25212755]
  Neuwald AF, Lanczycki CJ, Marchler-Bauer A. Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures. BMC Bioinformatics 2012 Jun 22;13(1):144. [Epub ahead of print] [PubMed PMID: 22726767] [Full Text]
  Derbyshire MK, Lanczycki CJ, Bryant SH, Marchler-Bauer A. Annotation of functional sites with the Conserved Domain Database. Database (Oxford) 2012 Mar 20;2012:bar058. Print 2012. [PubMed PMID: 22434827] [Full Text]
  Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, Deweese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9. Epub 2010 Nov 24. [PubMed PMID: 21109532] [Full Text]
  Fong JH, Marchler-Bauer A. CORAL: Aligning conserved core regions across domain families. Bioinformatics. 2009 Aug 1;25(15):1862-8. Epub 2009 May 26. [PubMed PMID: 19470584] [Full Text]
  Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res. 2009 Jan;37(Database issue):D205-10. Epub 2008 Nov 4. [PubMed PMID: 18984618] [Full Text]
  Fong JH, Marchler-Bauer A. Protein subfamily assignment using the Conserved Domain Database. BMC Res Notes. 2008 Nov 14;1(1):114. [PubMed PMID: 19014584] [Full Text]
  Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin J, Zhang D, Bryant SH. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D192-6. [PubMed PMID: 15608175] [Full Text]
  Panchenko AR, Kondrashov F, Bryant S. Prediction of functional sites by analysis of sequence and structure conservation. Protein Sci. 2004 Apr;13(4):884-92. [PubMed PMID: 15010543] [Full Text]
  Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res. 2003 Jan 1;31(1):383-7. [PubMed PMID: 12520028] [Full Text]
  Marchler-Bauer A, Panchenko AR, Ariel N, Bryant SH. Comparison of sequence and structure alignments for protein domains. Proteins. 2002 Aug 15;48(3):439-46. [PubMed PMID: 12112669] [Full Text]
  Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 2002 Jan 1;30(1):281-3. [PubMed PMID: 11752315] [Full Text]
 
 
 
Book Chapters
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  Sayers E, Bryant SH. Macromolecular Structure Databases. Chapter 3 IN The NCBI Handbook [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, 2002 Oct. 9 [revised 2003 Aug. 13]. [cited 2009 Feb 04]. Available from http://www.ncbi.nlm.nih.gov/books/NBK21095/ in Entrez Books (http://www.ncbi.nlm.nih.gov/books).
 
 
 
 Revised 25 November 2014