The conserved domain database in 2023.

Christopher J. Lanczycki

Jiyao Wang Farideh Chitsaz Myra K. Derbyshire Noreen R. Gonzales Marc Gwadz Shennan Lu Gabriele H. Marchler James S. Song Narmada Thanki Roxanne A. Yamashita Mingzhang Yang Dachuan Zhang Chanjuan Zheng Christopher J. Lanczycki Aron Marchler-Bauer The conserved domain database in 2023. 384-388 2023 January 51 Nucleic Acids Res. D1 https://doi.org/10.1093/nar/gkac1096 db/journals/nar/nar51.html#WangCDGGLMSTYYZZLM23

Eric W. Sayers Evan E. Bolton J. Rodney Brister Kathi Canese Jessica Chan Donald C. Comeau Ryan Connor Kathryn Funk Chris Kelly Sunghwan Kim 0002 Tom Madej Aron Marchler-Bauer Christopher J. Lanczycki Stacy Lathrop Zhiyong Lu Françoise Thibaud-Nissen Terence D. Murphy Lon Phan Yuri Skripchenko Tony Tse Jiyao Wang Rebecca Williams Barton W. Trawick Kim D. Pruitt Stephen T. Sherry Database resources of the national center for biotechnology information. 20-26 2022 50 Nucleic Acids Res. D1 https://doi.org/10.1093/nar/gkab1112 db/journals/nar/nar50.html#SayersBBCCCCFKK22

Wenjun Li Kathleen O'Neill Daniel H. Haft Michael DiCuccio Vyacheslav Chetvernin Azat Badretdin George Coulouris Farideh Chitsaz Myra K. Derbyshire A. Scott Durkin Noreen R. Gonzales Marc Gwadz Christopher J. Lanczycki James S. Song Narmada Thanki Jiyao Wang Roxanne A. Yamashita Mingzhang Yang Chanjuan Zheng Aron Marchler-Bauer Françoise Thibaud-Nissen RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. D1020-D1028 2021 49 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkaa1105 https://www.wikidata.org/entity/Q104059998 db/journals/nar/nar49.html#LiOHDCBCCDDGGLS21

Andrew F. Neuwald Christopher J. Lanczycki Theresa K. Hodges Aron Marchler-Bauer Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments. 2020 2020 Database J. Biol. Databases Curation https://doi.org/10.1093/database/baaa042 https://www.wikidata.org/entity/Q96161657 db/journals/biodb/biodb2020.html#NeuwaldLHM20

Jiyao Wang Philippe Youkharibache Dachuan Zhang Christopher J. Lanczycki Renata C. Geer Thomas Madej Lon Phan Minghong Ward Shennan Lu Gabriele H. Marchler Yanli Wang Stephen H. Bryant Lewis Y. Geer Aron Marchler-Bauer iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures. 131-135 2020 36 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btz502 https://www.wikidata.org/entity/Q92890371 db/journals/bioinformatics/bioinformatics36.html#WangYZLGMPWLMWB20

Shennan Lu Jiyao Wang Farideh Chitsaz Myra K. Derbyshire Renata C. Geer Noreen R. Gonzales Marc Gwadz David I. Hurwitz Gabriele H. Marchler James S. Song Narmada Thanki Roxanne A. Yamashita Mingzhang Yang Dachuan Zhang Chanjuan Zheng Christopher J. Lanczycki Aron Marchler-Bauer CDD/SPARCLE: the conserved domain database in 2020. D265-D268 2020 48 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkz991 https://www.wikidata.org/entity/Q91504235 db/journals/nar/nar48.html#LuWCDGGGHMSTYYZ20

Aron Marchler-Bauer Bo Yu 0016 Lianyi Han Jane He Christopher J. Lanczycki Shennan Lu Farideh Chitsaz Myra K. Derbyshire Renata C. Geer Noreen R. Gonzales Marc Gwadz David I. Hurwitz Fu Lu Gabriele H. Marchler James S. Song Narmada Thanki Zhouxi Wang Roxanne A. Yamashita Dachuan Zhang Chanjuan Zheng Lewis Y. Geer Stephen H. Bryant CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. D200-D203 2017 45 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkw1129 https://www.wikidata.org/entity/Q36207298 db/journals/nar/nar45.html#Marchler-BauerY17

Aron Marchler-Bauer Myra K. Derbyshire Noreen R. Gonzales Shennan Lu Farideh Chitsaz Lewis Y. Geer Renata C. Geer Jane He Marc Gwadz David I. Hurwitz Christopher J. Lanczycki Fu Lu Gabriele H. Marchler James S. Song Narmada Thanki Zhouxi Wang Roxanne A. Yamashita Dachuan Zhang Chanjuan Zheng Stephen H. Bryant CDD: NCBI's conserved domain database. 222-226 2015 43 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gku1221 https://www.wikidata.org/entity/Q29615740 db/journals/nar/nar43.html#Marchler-BauerDGLCGGHGHLLMSTWYZZB15

Thomas Madej Christopher J. Lanczycki Dachuan Zhang Paul A. Thiessen Renata C. Geer Aron Marchler-Bauer Stephen H. Bryant MMDB and VAST+: tracking structural similarities between macromolecular complexes. 297-303 2014 42 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkt1208 https://www.wikidata.org/entity/Q30356563 db/journals/nar/nar42.html#MadejLZTGMB14

Aron Marchler-Bauer Chanjuan Zheng Farideh Chitsaz Myra K. Derbyshire Lewis Y. Geer Renata C. Geer Noreen R. Gonzales Marc Gwadz David I. Hurwitz Christopher J. Lanczycki Fu Lu Shennan Lu Gabriele H. Marchler James S. Song Narmada Thanki Roxanne A. Yamashita Dachuan Zhang Stephen H. Bryant CDD: conserved domains and protein three-dimensional structure. 348-352 2013 41 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gks1243 https://www.wikidata.org/entity/Q30424248 db/journals/nar/nar41.html#Marchler-BauerZCDGGGGHLLLMSTYZB13

Myra K. Derbyshire Christopher J. Lanczycki Stephen H. Bryant Aron Marchler-Bauer Annotation of functional sites with the Conserved Domain Database. 2012 2012 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bar058 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308149/ https://www.wikidata.org/entity/Q34204358 db/journals/biodb/biodb2012.html#DerbyshireLBM12

Andrew F. Neuwald Christopher J. Lanczycki Aron Marchler-Bauer Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures. 144 2012 13 BMC Bioinform. https://doi.org/10.1186/1471-2105-13-144 https://www.wikidata.org/entity/Q34315125 db/journals/bmcbi/bmcbi13.html#NeuwaldLM12

Thomas Madej Kenneth J. Addess Jessica H. Fong Lewis Y. Geer Renata C. Geer Christopher J. Lanczycki Chunlei Liu 0002 Shennan Lu Aron Marchler-Bauer Anna R. Panchenko Jie Chen 0039 Paul A. Thiessen Yanli Wang Dachuan Zhang Stephen H. Bryant MMDB: 3D structures and macromolecular interactions. 461-464 2012 40 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkr1162 https://www.wikidata.org/entity/Q24622143 db/journals/nar/nar40.html#MadejAFGGLLLMPCTWZB12

Abhijit Chakraborty 0003 Sapan Mandloi Christopher J. Lanczycki Anna R. Panchenko Saikat Chakrabarti 0001 SPEER-SERVER: a web server for prediction of protein specificity determining sites. 242-248 2012 40 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gks559 https://www.wikidata.org/entity/Q36088556 db/journals/nar/nar40.html#ChakrabortyMLPC12

Aron Marchler-Bauer Shennan Lu John B. Anderson Farideh Chitsaz Myra K. Derbyshire Carol DeWeese-Scott Jessica H. Fong Lewis Y. Geer Renata C. Geer Noreen R. Gonzales Marc Gwadz David I. Hurwitz John D. Jackson Zhaoxi Ke Christopher J. Lanczycki Fu Lu Gabriele H. Marchler Mikhail Mullokandov Marina V. Omelchenko Cynthia L. Robertson James S. Song Narmada Thanki Roxanne A. Yamashita Dachuan Zhang Naigong Zhang Chanjuan Zheng Stephen H. Bryant CDD: a Conserved Domain Database for the functional annotation of proteins. 225-229 2011 39 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkq1189 https://www.wikidata.org/entity/Q24610576 db/journals/nar/nar39.html#Marchler-BauerLACDDFGGGGHJKLLMMORSTYZZZB11

Saikat Chakrabarti 0001 Christopher J. Lanczycki Anna R. Panchenko Teresa M. Przytycka Paul A. Thiessen Stephen H. Bryant State of the art: refinement of multiple sequence alignments. 3 2010 11 BMC Bioinform. https://doi.org/10.1186/1471-2105-11-3 https://www.wikidata.org/entity/Q59638139 db/journals/bmcbi/bmcbi11.html#ChakrabartiLPPTB10

Aron Marchler-Bauer John B. Anderson Farideh Chitsaz Myra K. Derbyshire Carol DeWeese-Scott Jessica H. Fong Lewis Y. Geer Renata C. Geer Noreen R. Gonzales Marc Gwadz Siqian He David I. Hurwitz John D. Jackson Zhaoxi Ke Christopher J. Lanczycki Cynthia A. Liebert Chunlei Liu 0002 Fu Lu Shennan Lu Gabriele H. Marchler Mikhail Mullokandov James S. Song Asba Tasneem Narmada Thanki Roxanne A. Yamashita Dachuan Zhang Naigong Zhang Stephen H. Bryant CDD: specific functional annotation with the Conserved Domain Database. 205-210 2009 37 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkn845 https://www.wikidata.org/entity/Q24655481 db/journals/nar/nar37.html#Marchler-BauerACDDFGGGGHHJKLLLLLMMSTTYZZB09

Aron Marchler-Bauer John B. Anderson Myra K. Derbyshire Carol DeWeese-Scott Noreen R. Gonzales Marc Gwadz Luning Hao Siqian He David I. Hurwitz John D. Jackson Zhaoxi Ke Dmitri M. Krylov Christopher J. Lanczycki Cynthia A. Liebert Chunlei Liu 0002 Fu Lu Shennan Lu Gabriele H. Marchler Mikhail Mullokandov James S. Song Narmada Thanki Roxanne A. Yamashita Jodie J. Yin Dachuan Zhang Stephen H. Bryant CDD: a conserved domain database for interactive domain family analysis. 237-240 2007 35 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkl951 https://www.wikidata.org/entity/Q24675724 db/journals/nar/nar35.html#Marchler-BauerADDGGHHHJKKLLLLLMMSTYYZB07

Saikat Chakrabarti 0001 Christopher J. Lanczycki Anna R. Panchenko Teresa M. Przytycka Paul A. Thiessen Stephen H. Bryant State of the art: refinement of multiple sequence alignments. 499 2006 7 BMC Bioinform. https://doi.org/10.1186/1471-2105-7-499 https://www.wikidata.org/entity/Q33263594 db/journals/bmcbi/bmcbi7.html#ChakrabartiLPPTB06

Aron Marchler-Bauer John B. Anderson Praveen F. Cherukuri Carol DeWeese-Scott Lewis Y. Geer Marc Gwadz Siqian He David I. Hurwitz John D. Jackson Zhaoxi Ke Christopher J. Lanczycki Cynthia A. Liebert Chunlei Liu 0002 Fu Lu Gabriele H. Marchler Mikhail Mullokandov Benjamin A. Shoemaker Vahan Simonyan James S. Song Paul A. Thiessen Roxanne A. Yamashita Jodie J. Yin Dachuan Zhang Stephen H. Bryant CDD: a Conserved Domain Database for protein classification. 192-196 2005 33 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gki069 https://www.wikidata.org/entity/Q24795306 db/journals/nar/nar33.html#Marchler-BauerACDGGHHJKLLLLMMSSSTYYZB05

Aron Marchler-Bauer John B. Anderson Carol DeWeese-Scott Natalie D. Fedorova Lewis Y. Geer Siqian He David I. Hurwitz John D. Jackson Aviva R. Jacobs Christopher J. Lanczycki Cynthia A. Liebert Chunlei Liu 0002 Thomas Madej Gabriele H. Marchler Raja Mazumder Anastasia N. Nikolskaya Anna R. Panchenko Bachoti S. Rao Benjamin A. Shoemaker Vahan Simonyan James S. Song Paul A. Thiessen Sona Vasudevan Yanli Wang Roxanne A. Yamashita Jodie J. Yin Stephen H. Bryant CDD: a curated Entrez database of conserved domain alignments. 383-387 2003 31 Nucleic Acids Res. 1 db/journals/nar/nar31.html#Marchler-BauerADFGHHJJLLLMMMNPRSSSTVWYYB03 https://doi.org/10.1093/nar/gkg087 https://www.wikidata.org/entity/Q29618556

Jie Chen 0039 John B. Anderson Carol DeWeese-Scott Natalie D. Fedorova Lewis Y. Geer Siqian He David I. Hurwitz John D. Jackson Aviva R. Jacobs Christopher J. Lanczycki Cynthia A. Liebert Chunlei Liu 0002 Thomas Madej Aron Marchler-Bauer Gabriele H. Marchler Raja Mazumder Anastasia N. Nikolskaya Bachoti S. Rao Anna R. Panchenko Benjamin A. Shoemaker Vahan Simonyan James S. Song Paul A. Thiessen Sona Vasudevan Yanli Wang Roxanne A. Yamashita Jodie J. Yin Stephen H. Bryant MMDB: Entrez's 3D-structure database. 474-477 2003 31 Nucleic Acids Res. 1 db/journals/nar/nar31.html#ChenADFGHHJJLLLMMMMNRPSSSTVWYYB03 https://doi.org/10.1093/nar/gkg086 https://www.wikidata.org/entity/Q55333533

Kenneth J. Addess John B. Anderson Azat Badretdin Evan BoltonEvan E. Bolton J. Rodney Brister Stephen H. Bryant Kathi Canese Saikat Chakrabarti 0001 Abhijit Chakraborty 0003 Jessica Chan Jie Chen 0039 Praveen F. Cherukuri Vyacheslav Chetvernin Farideh Chitsaz Donald C. Comeau Ryan Connor George Coulouris Myra K. Derbyshire Carol DeWeese-Scott Michael DiCuccio A. Scott Durkin Natalie D. Fedorova Jessica H. Fong Kathryn Funk Lewis Y. Geer Renata C. Geer Noreen R. Gonzales Marc Gwadz Daniel H. Haft Lianyi Han Luning Hao Jane He Siqian He Theresa K. Hodges David I. Hurwitz John D. Jackson Aviva R. Jacobs Zhaoxi Ke Chris Kelly Sunghwan Kim 0002 Dmitri M. Krylov Stacy Lathrop Wenjun Li Cynthia A. Liebert Chunlei Liu 0002 Fu Lu Shennan Lu Zhiyong Lu Thomas MadejTom Madej Sapan Mandloi Gabriele H. Marchler Aron Marchler-Bauer Raja Mazumder Mikhail Mullokandov Terence D. Murphy Andrew F. Neuwald Anastasia N. Nikolskaya Marina V. Omelchenko Kathleen O'Neill Anna R. Panchenko Lon Phan Kim D. Pruitt Teresa M. Przytycka Bachoti S. Rao Cynthia L. Robertson Eric W. Sayers Stephen T. Sherry Benjamin A. Shoemaker Vahan Simonyan Yuri Skripchenko James S. Song Asba Tasneem Narmada Thanki Françoise Thibaud-Nissen Paul A. Thiessen Barton W. Trawick Tony Tse Sona Vasudevan Jiyao Wang Yanli Wang Zhouxi Wang Minghong Ward Rebecca Williams Roxanne A. Yamashita Mingzhang Yang Jodie J. Yin Philippe Youkharibache Bo Yu 0016 Dachuan Zhang Naigong Zhang Chanjuan Zheng