Helen M. Berman

According to our database, Helen M. Berman authored at least 35 papers between 1980 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

Database Evolution, by Scientists, for Scientists: A Case Study.

Robert E. Schuler, Jitin Singla, Brinda Vallat, Kate L. White, Helen M. Berman, Carl Kesselman

Proceedings of the 19th IEEE International Conference on e-Science, 2023

2020

DNAproDB: an expanded database and web-based tool for structural analysis of DNA?protein complexes.

Jared M. Sagendorf, Nicholas Markarian, Helen M. Berman, Remo Rohs

Nucleic Acids Res., 2020

2019

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.

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

Nucleic Acids Res., 2019

Open access to research artifacts: Implementing the next generation data management plan.

Victoria Stodden, Vicki Ferrini, Margaret J. Gabanyi, Kerstin A. Lehnert, John Morton, Helen M. Berman

Proceedings of the Information... Anyone, Anywhere, Any Time, Any Way, 2019

2018

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

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

Database J. Biol. Databases Curation, 2018

2017

DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.

Jared M. Sagendorf, Helen M. Berman, Remo Rohs

Nucleic Acids Res., 2017

The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

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

Nucleic Acids Res., 2017

2016

EMDataBank unified data resource for 3DEM.

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

Nucleic Acids Res., 2016

2015

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

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

Nucleic Acids Res., 2015

RCSB PDB <i>Mobile</i>: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.

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

Bioinform., 2015

2014

The Nucleic Acid Database: new features and capabilities.

Buvaneswari Coimbatore Narayanan, John D. Westbrook, Saheli Ghosh, Anton I. Petrov, Blake A. Sweeney, Craig L. Zirbel, Neocles Leontis, Helen M. Berman

Nucleic Acids Res., 2014

The Protein Data Bank archive as an open data resource.

Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley

J. Comput. Aided Mol. Des., 2014

2013

The RCSB Protein Data Bank: new resources for research and education.

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

Nucleic Acids Res., 2013

Chemical annotation of small and peptide-like molecules at the Protein Data Bank.

Jasmine Young, Zukang Feng, Dimitris Dimitropoulos, Raul Sala, John D. Westbrook, Marina Zhuravleva, Chenghua Shao, Martha Quesada, Ezra Peisach, Helen M. Berman

Database J. Biol. Databases Curation, 2013

2011

The RCSB Protein Data Bank: redesigned web site and web services.

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

Nucleic Acids Res., 2011

EMDataBank.org: unified data resource for CryoEM.

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

Nucleic Acids Res., 2011

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.

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

Database J. Biol. Databases Curation, 2011

Workshop Introduction.

Steven J. Ludtke, Catherine L. Lawson, Gerard J. Kleywegt, Helen M. Berman, Wah Chiu

Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011

2009

The protein structure initiative structural genomics knowledgebase.

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

Nucleic Acids Res., 2009

2008

Remediation of the protein data bank archive.

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

Nucleic Acids Res., 2008

2007

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.

Helen M. Berman, Kim Henrick, Haruki Nakamura, John L. Markley

Nucleic Acids Res., 2007

2006

The RCSB PDB information portal for structural genomics.

Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman

Nucleic Acids Res., 2006

2005

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema.

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

Nucleic Acids Res., 2005

PDBML: the representation of archival macromolecular structure data in XML.

John D. Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman

Bioinform., 2005

2004

The distribution and query systems of the RCSB Protein Data Bank.

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

Nucleic Acids Res., 2004

Ligand Depot: a data warehouse for ligands bound to macromolecules.

Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred, Helen M. Berman, John D. Westbrook

Bioinform., 2004

TargetDB: a target registration database for structural genomics projects.

Li Chen, Rose Oughtred, Helen M. Berman, John D. Westbrook

Bioinform., 2004

The Protein Data Bank and lessons in data management.

Philip E. Bourne, John D. Westbrook, Helen M. Berman

Briefings Bioinform., 2004

2003

The Need for Dictionaries, Ontologies, and Controlled Vocabularies.

Helen M. Berman, John D. Westbrook

OMICS, 2003

Tools for the automatic identification and classification of RNA base pairs.

Huanwang Yang, Fabrice Jossinet, Neocles Leontis, Li Chen, John D. Westbrook, Helen M. Berman, Eric Westhof

Nucleic Acids Res., 2003

The Protein Data Bank and structural genomics.

John D. Westbrook, Zukang Feng, Li Chen, Huanwang Yang, Helen M. Berman

Nucleic Acids Res., 2003

2002

The Protein Data Bank: unifying the archive.

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

Nucleic Acids Res., 2002

2001

The PDB data uniformity project.

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

Nucleic Acids Res., 2001

2000

The Protein Data Bank.

Helen M. Berman, John D. Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne

Nucleic Acids Res., 2000

1980

The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments.

H. S. Shieh, Helen M. Berman, M. Dabrow, Stephen Neidle

Nucleic Acids Res., 1980