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Helen M. Berman
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Journal Articles
- 2020
- [j32]Jared M. Sagendorf, Nicholas Markarian, Helen M. Berman, Remo Rohs
:
DNAproDB: an expanded database and web-based tool for structural analysis of DNA?protein complexes. Nucleic Acids Res. 48(Database-Issue): D277-D287 (2020) - 2019
- [j31]Stephen K. Burley, Helen M. Berman
, Charmi Bhikadiya
, Chunxiao Bi, Li Chen, Luigi Di Costanzo
, Cole H. Christie, Kenneth Dalenberg, Jose M. Duarte, Shuchismita Dutta
, Zukang Feng, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic
, Dmytro Guzenko, Brian P. Hudson
, Tara Kalro, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Periskova, Andreas Prlic, Christopher Randle, Alexander S. Rose
, Peter W. Rose
, Raul Sala, Monica Sekharan, Chenghua Shao
, Lihua Tan, Yi-Ping Tao, Yana Valasatava
, Maria Voigt, John D. Westbrook, Jesse Woo, Huanwang Yang, Jasmine Young
, Marina Zhuravleva, Christine Zardecki
:
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Res. 47(Database-Issue): D464-D474 (2019) - 2018
- [j30]Jasmine Young
, John D. Westbrook, Zukang Feng, Ezra Peisach
, Irina Persikova
, Raul Sala, Sanchayita Sen, John M. Berrisford
, Jawahar Swaminathan, Thomas J. Oldfield, Aleksandras Gutmanas, Reiko Igarashi, David R. Armstrong
, Kumaran Baskaran
, Li Chen, Minyu Chen, Alice R. Clark, Luigi Di Costanzo
, Dimitris Dimitropoulos, Guanghua Gao, Sutapa Ghosh, Swanand P. Gore, Vladimir Guranovic
, Pieter M. S. Hendrickx
, Brian P. Hudson
, Yasuyo Ikegawa, Yumiko Kengaku, Catherine L. Lawson
, Yuhe Liang, Lora Mak
, Abhik Mukhopadhyay, Buvaneswari Coimbatore Narayanan, Kayoko Nishiyama, Ardan Patwardhan
, Gaurav Sahni, Eduardo Sanz-García, Junko Sato, Monica Sekharan, Chenghua Shao
, Oliver S. Smart, Lihua Tan, Glen van Ginkel
, Huanwang Yang, Marina Zhuravleva, John L. Markley, Haruki Nakamura, Genji Kurisu
, Gerard J. Kleywegt, Sameer Velankar, Helen M. Berman, Stephen K. Burley:
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database J. Biol. Databases Curation 2018: bay002 (2018) - 2017
- [j29]Peter W. Rose
, Andreas Prlic
, Ali Altunkaya, Chunxiao Bi, Anthony R. Bradley, Cole H. Christie, Luigi Di Costanzo
, Jose M. Duarte
, Shuchismita Dutta
, Zukang Feng, Rachel Kramer Green, David S. Goodsell, Brian P. Hudson
, Tara Kalro, Robert Lowe, Ezra Peisach
, Christopher Randle, Alexander S. Rose, Chenghua Shao
, Yi-Ping Tao, Yana Valasatava
, Maria Voigt, John D. Westbrook, Jesse Woo, Huanwang Yang, Jasmine Young
, Christine Zardecki
, Helen M. Berman
, Stephen K. Burley
:
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res. 45(Database-Issue): D271-D281 (2017) - [j28]Jared M. Sagendorf, Helen M. Berman
, Remo Rohs
:
DNAproDB: an interactive tool for structural analysis of DNA-protein complexes. Nucleic Acids Res. 45(Webserver-Issue): W89-W97 (2017) - 2016
- [j27]Catherine L. Lawson
, Ardan Patwardhan, Matthew L. Baker, Corey Hryc
, Eduardo Sanz-García, Brian P. Hudson
, Ingvar C. Lagerstedt
, Steven J. Ludtke
, Grigore Pintilie, Raul Sala, John D. Westbrook, Helen M. Berman
, Gerard J. Kleywegt, Wah Chiu:
EMDataBank unified data resource for 3DEM. Nucleic Acids Res. 44(Database-Issue): 396-403 (2016) - 2015
- [j26]Gregory B. Quinn, Chunxiao Bi, Cole H. Christie, Kyle Pang, Andreas Prlic
, Takanori Nakane
, Christine Zardecki
, Maria Voigt, Helen M. Berman, Philip E. Bourne, Peter W. Rose
:
RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. Bioinform. 31(1): 126-127 (2015) - [j25]Peter W. Rose
, Andreas Prlic
, Chunxiao Bi, Wolfgang Bluhm, Cole H. Christie, Shuchismita Dutta
, Rachel Kramer Green, David S. Goodsell, John D. Westbrook, Jesse Woo, Jasmine Young
, Christine Zardecki
, Helen M. Berman
, Philip E. Bourne
, Stephen K. Burley
:
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res. 43(Database-Issue): 345-356 (2015) - 2014
- [j24]Helen M. Berman
, Gerard J. Kleywegt
, Haruki Nakamura, John L. Markley:
The Protein Data Bank archive as an open data resource. J. Comput. Aided Mol. Des. 28(10): 1009-1014 (2014) - [j23]Buvaneswari Coimbatore Narayanan, John D. Westbrook, Saheli Ghosh, Anton I. Petrov, Blake A. Sweeney
, Craig L. Zirbel, Neocles Leontis, Helen M. Berman
:
The Nucleic Acid Database: new features and capabilities. Nucleic Acids Res. 42(Database-Issue): 114-122 (2014) - 2013
- [j22]Jasmine Young
, Zukang Feng, Dimitris Dimitropoulos, Raul Sala, John D. Westbrook, Marina Zhuravleva, Chenghua Shao
, Martha Quesada, Ezra Peisach
, Helen M. Berman
:
Chemical annotation of small and peptide-like molecules at the Protein Data Bank. Database J. Biol. Databases Curation 2013 (2013) - [j21]Peter W. Rose
, Chunxiao Bi, Wolfgang Bluhm, Cole H. Christie, Dimitris Dimitropoulos, Shuchismita Dutta
, Rachel Kramer Green, David S. Goodsell, Andreas Prlic
, Martha Quesada, Greg B. Quinn, Alexander G. Ramos, John D. Westbrook, Jasmine Young
, Christine Zardecki
, Helen M. Berman
, Philip E. Bourne:
The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 41(Database-Issue): 475-482 (2013) - 2011
- [j20]Wolfgang Bluhm, Bojan Beran, Chunxiao Bi, Dimitris Dimitropoulos, Andreas Prlic
, Greg B. Quinn, Peter W. Rose
, Chaitali Shah, Jasmine Young
, Benjamin T. Yukich, Helen M. Berman
, Philip E. Bourne:
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. Database J. Biol. Databases Curation 2011 (2011) - [j19]Peter W. Rose
, Bojan Beran, Chunxiao Bi, Wolfgang Bluhm, Dimitris Dimitropoulos, David S. Goodsell, Andreas Prlic
, Martha Quesada, Greg B. Quinn, John D. Westbrook, Jasmine Young
, Benjamin T. Yukich, Christine Zardecki
, Helen M. Berman
, Philip E. Bourne:
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 39(Database-Issue): 392-401 (2011) - [j18]Catherine L. Lawson
, Matthew L. Baker, Christoph Best, Chunxiao Bi, Matthew T. Dougherty, Powei Feng, Glen van Ginkel
, Batsal Devkota, Ingvar C. Lagerstedt
, Steven J. Ludtke
, Richard H. Newman, Thomas J. Oldfield, Ian Rees, Gaurav Sahni, Raul Sala, Sameer Velankar
, Joe D. Warren, John D. Westbrook, Kim Henrick, Gerard J. Kleywegt
, Helen M. Berman
, Wah Chiu:
EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res. 39(Database-Issue): 456-464 (2011) - 2009
- [j17]Helen M. Berman
, John D. Westbrook, Margaret J. Gabanyi
, Wendy Tao, Raship Shah, Andrei Kouranov, Torsten Schwede
, Konstantin Arnold, Florian Kiefer, Lorenza Bordoli, Jürgen Kopp, Michael Podvinec
, Paul D. Adams
, Lester G. Carter, Wladek Minor
, Rajesh Nair, Joshua La Baer:
The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res. 37(Database-Issue): 365-368 (2009) - 2008
- [j16]Kim Henrick, Zukang Feng, Wolfgang Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta
, Judith L. Flippen-Anderson, John M. C. Ionides, Chisa Kamada, Eugene Krissinel, Catherine L. Lawson
, John L. Markley, Haruki Nakamura, Richard H. Newman, Yukiko Shimizu, Jawahar Swaminathan
, Sameer Velankar
, Jeramia Ory
, Eldon L. Ulrich, Wim F. Vranken
, John D. Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young
, Muhammed Yousufuddin, Helen M. Berman
:
Remediation of the protein data bank archive. Nucleic Acids Res. 36(Database-Issue): 426-433 (2008) - 2007
- [j15]Helen M. Berman
, Kim Henrick, Haruki Nakamura, John L. Markley:
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 35(Database-Issue): 301-303 (2007) - 2006
- [j14]Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman
:
The RCSB PDB information portal for structural genomics. Nucleic Acids Res. 34(Database-Issue): 302-305 (2006) - 2005
- [j13]John D. Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman
:
PDBML: the representation of archival macromolecular structure data in XML. Bioinform. 21(7): 988-992 (2005) - [j12]Nita Deshpande, Kenneth J. Addess, Wolfgang Bluhm, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie Xie, Li Chen, Zukang Feng, Rachel Kramer Green, Judith L. Flippen-Anderson, John D. Westbrook, Helen M. Berman, Philip E. Bourne:
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res. 33(Database-Issue): 233-237 (2005) - 2004
- [j11]Philip E. Bourne, John D. Westbrook, Helen M. Berman:
The Protein Data Bank and lessons in data management. Briefings Bioinform. 5(1): 23-30 (2004) - [j10]Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred
, Helen M. Berman
, John D. Westbrook:
Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinform. 20(13): 2153-2155 (2004) - [j9]Li Chen, Rose Oughtred
, Helen M. Berman
, John D. Westbrook:
TargetDB: a target registration database for structural genomics projects. Bioinform. 20(16): 2860-2862 (2004) - [j8]Philip E. Bourne, Kenneth J. Addess, Wolfgang Bluhm, Li Chen, Nita Deshpande, Zukang Feng, Ward Fleri, Rachel Kramer Green, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Helge Weissig, John D. Westbrook, Helen M. Berman
:
The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res. 32(Database-Issue): 223-225 (2004) - 2003
- [j7]John D. Westbrook, Zukang Feng, Li Chen, Huanwang Yang, Helen M. Berman:
The Protein Data Bank and structural genomics. Nucleic Acids Res. 31(1): 489-491 (2003) - [j6]Huanwang Yang, Fabrice Jossinet, Neocles Leontis, Li Chen, John D. Westbrook, Helen M. Berman, Eric Westhof:
Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 31(13): 3450-3460 (2003) - [j5]Helen M. Berman
, John D. Westbrook
:
The Need for Dictionaries, Ontologies, and Controlled Vocabularies. OMICS 7(1): 9-10 (2003) - 2002
- [j4]John D. Westbrook
, Zukang Feng, Shri Jain, T. N. Bhat, Narmada Thanki, Veerasamy Ravichandran, Gary Gilliland, Wolfgang Bluhm, Helge Weissig, Douglas S. Greer, Philip E. Bourne, Helen M. Berman:
The Protein Data Bank: unifying the archive. Nucleic Acids Res. 30(1): 245-248 (2002) - 2001
- [j3]T. N. Bhat, Philip E. Bourne, Zukang Feng, Gary Gilliland, Shri Jain, Veerasamy Ravichandran, Bohdan Schneider
, Kata Schneider, Narmada Thanki, Helge Weissig, John D. Westbrook, Helen M. Berman:
The PDB data uniformity project. Nucleic Acids Res. 29(1): 214-218 (2001) - 2000
- [j2]Helen M. Berman
, John D. Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne
:
The Protein Data Bank. Nucleic Acids Res. 28(1): 235-242 (2000) - 1980
- [j1]H. S. Shieh, Helen M. Berman, M. Dabrow, Stephen Neidle:
The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments. Nucleic Acids Res. 8(1): 85-97 (1980)
Conference and Workshop Papers
- 2023
- [c3]Robert E. Schuler
, Jitin Singla, Brinda Vallat, Kate L. White, Helen M. Berman, Carl Kesselman:
Database Evolution, by Scientists, for Scientists: A Case Study. e-Science 2023: 1-10 - 2019
- [c2]Victoria Stodden, Vicki Ferrini
, Margaret J. Gabanyi, Kerstin A. Lehnert, John Morton, Helen M. Berman:
Open access to research artifacts: Implementing the next generation data management plan. ASIST 2019: 481-485 - 2011
- [c1]Steven J. Ludtke, Catherine L. Lawson, Gerard J. Kleywegt, Helen M. Berman, Wah Chiu:
Workshop Introduction. Pacific Symposium on Biocomputing 2011: 369
Coauthor Index
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