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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] |
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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]
(Note: The NAR 2011 article on the Conserved Domain Database, listed above, discusses Batch CD-Search. Please cite that paper if using the Batch CD-Search tool.) |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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