Helen M. Berman

Publication Activity (10 Years)

Years Active: 1980-2023
Publications (10 Years): 8

Top Topics

Structural Analysis

Protein Data Bank

Protein Complexes

Top Venues

Nucleic Acids Res.

Database J. Biol. Databases Curation

Publications

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)
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) (2020)
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) (2019)
Victoria Stodden, Vicki Ferrini, Margaret J. Gabanyi, Kerstin Lehnert, John Morton, Helen M. Berman
Open access to research artifacts: Implementing the next generation data management plan. ASIST (2019)
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 (2018)
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) (2017)
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) (2017)
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) (2016)
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
: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. Bioinform. 31 (1) (2015)
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) (2015)
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) (2014)
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) (2014)
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)
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) (2013)
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)
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) (2011)
Steven J. Ludtke, Catherine L. Lawson, Gerard J. Kleywegt, Helen M. Berman, Wah Chiu
Workshop Introduction. Pacific Symposium on Biocomputing (2011)
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) (2011)
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) (2009)
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) (2008)
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) (2007)
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) (2006)
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) (2005)
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) (2005)
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) (2004)
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) (2004)
Philip E. Bourne, John D. Westbrook, Helen M. Berman
The Protein Data Bank and lessons in data management. Briefings Bioinform. 5 (1) (2004)
Li Chen, Rose Oughtred, Helen M. Berman, John D. Westbrook
TargetDB: a target registration database for structural genomics projects. Bioinform. 20 (16) (2004)
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) (2003)
Helen M. Berman, John D. Westbrook
The Need for Dictionaries, Ontologies, and Controlled Vocabularies. OMICS 7 (1) (2003)
John D. Westbrook, Zukang Feng, Li Chen, Huanwang Yang, Helen M. Berman
The Protein Data Bank and structural genomics. Nucleic Acids Res. 31 (1) (2003)
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) (2002)
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) (2001)
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) (2000)
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) (1980)