Conserved Domains and Protein Classification
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 Citing the Resources		  
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  Conserved Domain Database (CDD)
  Wang J, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Yang M, Zhang D, Zheng C, Lanczycki CJ, Marchler-Bauer A.The conserved domain database in 2023. Nucleic Acids Res. 2022 Jan 6;51(D1):D384-D388. doi: 10.1093/nar/gkac1096. [PubMed PMID: 36477806] [Full Text at Oxford Academic]Click here to read
   
  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 at Oxford Academic]

Note: If using Batch CD-Search, please also cite a second article, which discussed the launch of that resource:
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. doi: 10.1093/nar/gkq1189. Epub 2010 Nov 24. [PubMed PMID: 21109532] [Full Text at Oxford Academic] [Full text in PubMed Central]		 Click here to read
   
  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 at Oxford Academic] Click here to read
   
  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 at CSH Press] Click here to read
   
  Subfamily Protein Architecture Labeling Engine (SPARCLE)
  Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Marchler GH, Song JS, Thanki N, Yamashita RA, Yang M, Zhang D, Zheng C, Lanczycki CJ, Marchler-Bauer A. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 2020 Jan 8;48(D1):D265-D268. doi: 10.1093/nar/gkz991. Epub 2019 Nov 28. [PubMed PMID: 31777944] [Full Text at Oxford Academic] Click here to read
   
   
 
 
 
 Additional Journal Articles		 back to top
 
  Sayers EW, Beck J, Bolton EE, Brister JR, Chan J, Comeau DC, Connor R, DiCuccio M, Farrell CM, Feldgarden M, Fine AM, Funk K, Hatcher E, Hoeppner M, Kane M, Kannan S, Katz KS, Kelly C, Klimke W, Kim S, Kimchi A, Landrum M, Lathrop S, Lu Z, Malheiro A, Marchler-Bauer A, Murphy TD, Phan L, Prasad AB, Pujar S, Sawyer A, Schmieder E, Schneider VA, Schoch CL, Sharma S, Thibaud-Nissen F, Trawick BW, Venkatapathi T, Wang J, Pruitt KD, Sherry ST. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2024 Jan 5;52(D1):D33-D43. doi: 10.1093/nar/gkad1044. [PubMed PMID: 37994677] [Full Text at Oxford Academic]  Click here to read
  Wang J, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Yang M, Zhang D, Zheng C, Lanczycki CJ, Marchler-Bauer A. The conserved domain database in 2023. Nucleic Acids Res. 2023 Jan 6;51(D1):D384-D388. doi: 10.1093/nar/gkac1096. [PubMed PMID: 36477806] [Full Text at Oxford Academic]  Click here to read
  Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC, Farrell CM, Feldgarden M, Fine AM, Funk K, Hatcher E, Kannan S, Kelly C, Kim S, Klimke W, Landrum MJ, Lathrop S, Lu Z, Madden TL, Malheiro A, Marchler-Bauer A, Murphy TD, Phan L, Pujar S, Rangwala SH, Schneider VA, Tse T, Wang J, Ye J, Trawick BW, Pruitt KD, Sherry ST. Database resources of the National Center for Biotechnology Information in 2023. Nucleic Acids Res. 2023 Jan 6;51(D1):D29-D38. doi: 10.1093/nar/gkac1032. [PubMed PMID: 36370100] [Full Text at Oxford Academic]  Click here to read
  Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL, Salazar GA, Bileschi ML, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A. InterPro in 2022. Nucleic Acids Res. 2023 Jan 6;51(D1):D418-D427. doi: 10.1093/nar/gkac993. [PubMed PMID: 36350672] [Full Text at Oxford Academic]  Click here to read
  de Crecy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O'Donoghue S, Orengo C, O'Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. A roadmap for the functional annotation of protein families: a community perspective. Database (Oxford). 2022 Aug 12;2022:baac062. doi: 10.1093/database/baac062. [PubMed PMID: 35961013] [Full Text at Oxford Academic]  Click here to read
  Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC, Connor R, Funk K, Kelly C, Kim S, Madej T, Marchler-Bauer A, Lanczycki C, Lathrop S, Lu Z, Thibaud-Nissen F, Murphy T, Phan L, Skripchenko Y, Tse T, Wang J, Williams R, Trawick BW, Pruitt KD, Sherry ST. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2021 Dec 1. doi: 10.1093/nar/gkab1112. [PubMed PMID: 34850941] [Full Text at Oxford Academic]  Click here to read
  Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, Coulouris G, Chitsaz F, Derbyshire MK, Durkin AS, Gonzales NR, Gwadz M, Lanczycki CJ, Song JS, Thanki N, Wang J, Yamashita RA, Yang M, Zheng C, Marchler-Bauer A, Thibaud-Nissen F. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res. 2020 Dec 3:gkaa1105. doi: 10.1093/nar/gkaa1105. [Online ahead of print] [PubMed PMID: 33270901] [Full Text at Oxford Academic]  Click here to read
  Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 2020 Nov 6:gkaa977. doi: 10.1093/nar/gkaa977. [PubMed PMID: 33156333] [Full Text at Oxford Academic]  Click here to read
  Yang M, Derbyshire MK, Yamashita RA, Marchler-Bauer A. NCBI's Conserved Domain Database and Tools for Protein Domain Analysis. Curr Protoc Bioinformatics 2020 Mar;69(1):e90. doi: 10.1002/cpbi.90. [PubMed PMID: 31851420] [Full Text at Wiley]  Click here to read
  Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Marchler GH, Song JS, Thanki N, Yamashita RA, Yang M, Zhang D, Zheng C, Lanczycki CJ, Marchler-Bauer A. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 2020 Jan 8;48(D1):D265-D268. doi: 10.1093/nar/gkz991. Epub 2019 Nov 28. [PubMed PMID: 31777944] [Full Text at Oxford Academic] Click here to read
  Neuwald AF, Lanczycki CJ, Hodges TK, Marchler-Bauer A. Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments. Database (Oxford) 2020 Jan 1;2020. pii: baaa042. doi: 10.1093/database/baaa042. [PubMed PMID: 32500917] [Full Text at Oxford Academic] Click here to read
  Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2019 Jan 8;47(D1):D351-D360. doi: 10.1093/nar/gky1100. [PubMed PMID: 30398656] [Full Text at Oxford Academic] Click here to read
  Islamaj R, Wilbur WJ, Xie N, Gonzales NR, Thanki N, Yamashita R, Zheng C, Marchler-Bauer A, Lu Z. PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database. Database (Oxford) 2019 Jan 1;2019. pii: baz064. doi: 10.1093/database/baz064. [PubMed PMID: 31267135] [Full Text at Oxford Academic] Click here to read
  Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V, O'Neill K, Li W, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu F, Marchler GH, Song JS, Thanki N, Yamashita RA, Zheng C, Thibaud-Nissen F, Geer LY, Marchler-Bauer A, Pruitt KD. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res. 2017 Nov 3. doi: 10.1093/nar/gkx1068. [Epub ahead of print] [PubMed PMID: 29112715] [Full Text at Oxford Academic]
  Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Geer LY, Bryant SH. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2017 Jan 4;45(D1):D200-D203. doi: 10.1093/nar/gkw1129. Epub 2016 Nov 29. [PubMed PMID: 27899674] [Full Text at Oxford Academic] Click here to read
  Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi: 10.1093/nar/gkw1107. Epub 2016 Nov 29. [PubMed PMID: 27899635] [Full Text at Oxford Academic] Click here to read
  Derbyshire MK, Gonzales NR, Lu S, He J, Marchler GH, Wang Z, Marchler-Bauer A. Improving the consistency of domain annotation within the Conserved Domain Database. Database (Oxford) 2015 Mar 12; 2015. pii: bav012. doi: 10.1093/database/bav012. Print 2015. [PubMed PMID: 25767294] [Full Text at Oxford Academic] Click here to read
  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. 2015 Jan 28;43(Database issue):D222-2. doi: 10.1093/nar/gku1221. Epub 2014 Nov 20. [PubMed PMID: 25414356] [Full Text at Oxford Academic] Click here to read
  Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE. cddApp: A Cytoscape App for Accessing the NCBI Conserved Domain Database. Bioinformatics 2015 Jan 1;31(1):134-6. doi: 10.1093/bioinformatics/btu605. Epub 2014 Sep 10. [PubMed PMID: 25212755][Full Text at Oxford Academic] Click here to read
  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. doi: 10.1093/nar/gks1243. Epub 2012 Nov 28. [PubMed PMID: 23197659] [Full Text at Oxford Academic] Click here to read
  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. doi: 10.1186/1471-2105-13-144. [PubMed PMID: 22726767] [Full Text at BioMed Central] Click here to read
  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. doi: https://doi.org/10.1093/database/bar058. [PubMed PMID: 22434827] [Full Text at Oxford Academic] Click here to read
  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. doi: 10.1093/nar/gkq1189. Epub 2010 Nov 24. [PubMed PMID: 21109532] [Full Text at Oxford Academic] Click here to read
  Fong JH, Marchler-Bauer A. CORAL: Aligning conserved core regions across domain families. Bioinformatics. 2009 Aug 1;25(15):1862-8. doi: 10.1093/bioinformatics/btp334. Epub 2009 May 26. [PubMed PMID: 19470584] [Full Text at Oxford Academic] Click here to read
  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. doi: 10.1093/nar/gkn845. Epub 2008 Nov 4. [PubMed PMID: 18984618] [Full Text at Oxford Academic] Click here to read
  Fong JH, Marchler-Bauer A. Protein subfamily assignment using the Conserved Domain Database. BMC Res Notes. 2008 Nov 14;1(1):114. doi: 10.1186/1756-0500-1-114. [PubMed PMID: 19014584] [Full Text at BioMed Central] Click here to read
  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. doi: 10.1093/nar/gki069. [PubMed PMID: 15608175] [Full Text at Oxford Academic] Click here to read
  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. doi: 10.1110/ps.03465504. [PubMed PMID: 15010543] [Full Text at Wiley Online Library] Click here to read
  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. doi: 10.1093/nar/gkg087. [PubMed PMID: 12520028] [Full Text at Oxford Academic] Click here to read
  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 at Wiley Online Library]  
  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 at Oxford Academic] Click here to read
 
 
 
 Book Chapters		 back to top
 
  Sayers E. NCBI Protein Resources. IN The NCBI Handbook, 2nd edition [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, 2013 Nov. 12, 2013 [revised 2013 Nov. 21]. [cited 2017 Feb 02]. Available from https://www.ncbi.nlm.nih.gov/books/NBK169830/ in Entrez Books (https://www.ncbi.nlm.nih.gov/books).
  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 https://www.ncbi.nlm.nih.gov/books/NBK21095/ in Entrez Books (https://www.ncbi.nlm.nih.gov/books).
 
 
 
Revised 21 November 2024