Conserved Domain Database (CDD) Publications

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3D Macromolecular Structures

Conserved Domains

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Conserved Domains and Protein Classification

Citing the Resources

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	Conserved Domain Database (CDD)
		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.

	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.

	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.

	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.

Additional Journal Articles

		Fong JH, Marchler-Bauer A. CORAL: Aligning conserved core regions across domain families. Bioinformatics. 2009 May 26 [Epub ahead of print]
		Fong JH, Marchler-Bauer A. Protein subfamily assignment using the Conserved Domain Database. BMC Res Notes. 2008 Nov 14;1(1):114. [Epub ahead of print]
		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.
		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.
		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.
		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.
		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.

Book Chapters

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/bv.fcgi?rid=handbook.chapter.ch3 in Entrez Books (http://www.ncbi.nlm.nih.gov/sites/entrez?db=books).

| Revised 09 September 2009 |

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