Helen M. Berman

35 papers B 1Misc 1Journal 32Unranked 1
YearRankTypeTitle / Venue / Authors
2023 B conf
Database Evolution, by Scientists, for Scientists: A Case Study.
e-Science
Robert E. Schuler, Jitin Singla, Brinda Vallat, Kate L. White, Helen M. Berman, Carl Kesselman
2020 J jnl
DNAproDB: an expanded database and web-based tool for structural analysis of DNA?protein complexes.
Nucleic Acids Res.
Jared M. Sagendorf, Nicholas Markarian, Helen M. Berman, Remo Rohs
2019 — conf
Open access to research artifacts: Implementing the next generation data management plan.
ASIST
Victoria Stodden, Vicki Ferrini, Margaret J. Gabanyi, Kerstin A. Lehnert, John Morton, Helen M. Berman
2019 J jnl
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.
Nucleic Acids Res.
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
2018 J jnl
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.
Database J. Biol. Databases Curation
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
2017 J jnl
DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.
Nucleic Acids Res.
Jared M. Sagendorf, Helen M. Berman, Remo Rohs
2017 J jnl
The RCSB protein data bank: integrative view of protein, gene and 3D structural information.
Nucleic Acids Res.
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
2016 J jnl
EMDataBank unified data resource for 3DEM.
Nucleic Acids Res.
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
2015 J jnl
RCSB PDB
Bioinform.
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
2015 J jnl
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.
Nucleic Acids Res.
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
2014 J jnl
The Nucleic Acid Database: new features and capabilities.
Nucleic Acids Res.
Buvaneswari Coimbatore Narayanan, John D. Westbrook, Saheli Ghosh, Anton I. Petrov, Blake A. Sweeney, Craig L. Zirbel, Neocles Leontis, Helen M. Berman
2014 J jnl
The Protein Data Bank archive as an open data resource.
J. Comput. Aided Mol. Des.
Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley
2013 J jnl
Chemical annotation of small and peptide-like molecules at the Protein Data Bank.
Database J. Biol. Databases Curation
Jasmine Young, Zukang Feng, Dimitris Dimitropoulos, Raul Sala, John D. Westbrook, Marina Zhuravleva, Chenghua Shao, Martha Quesada, Ezra Peisach, Helen M. Berman
2013 J jnl
The RCSB Protein Data Bank: new resources for research and education.
Nucleic Acids Res.
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
2011 J jnl
EMDataBank.org: unified data resource for CryoEM.
Nucleic Acids Res.
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
2011 J jnl
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.
Database J. Biol. Databases Curation
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
2011 J jnl
The RCSB Protein Data Bank: redesigned web site and web services.
Nucleic Acids Res.
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
2011 Misc conf
Workshop Introduction.
Pacific Symposium on Biocomputing
Steven J. Ludtke, Catherine L. Lawson, Gerard J. Kleywegt, Helen M. Berman, Wah Chiu
2009 J jnl
The protein structure initiative structural genomics knowledgebase.
Nucleic Acids Res.
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
2008 J jnl
Remediation of the protein data bank archive.
Nucleic Acids Res.
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
2007 J jnl
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.
Nucleic Acids Res.
Helen M. Berman, Kim Henrick, Haruki Nakamura, John L. Markley
2006 J jnl
The RCSB PDB information portal for structural genomics.
Nucleic Acids Res.
Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman
2005 J jnl
PDBML: the representation of archival macromolecular structure data in XML.
Bioinform.
John D. Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman
2005 J jnl
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema.
Nucleic Acids Res.
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
2004 J jnl
Ligand Depot: a data warehouse for ligands bound to macromolecules.
Bioinform.
Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred, Helen M. Berman, John D. Westbrook
2004 J jnl
TargetDB: a target registration database for structural genomics projects.
Bioinform.
Li Chen, Rose Oughtred, Helen M. Berman, John D. Westbrook
2004 J jnl
The Protein Data Bank and lessons in data management.
Briefings Bioinform.
Philip E. Bourne, John D. Westbrook, Helen M. Berman
2004 J jnl
The distribution and query systems of the RCSB Protein Data Bank.
Nucleic Acids Res.
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
2003 J jnl
The Need for Dictionaries, Ontologies, and Controlled Vocabularies.
OMICS
Helen M. Berman, John D. Westbrook
2003 J jnl
The Protein Data Bank and structural genomics.
Nucleic Acids Res.
John D. Westbrook, Zukang Feng, Li Chen, Huanwang Yang, Helen M. Berman
2003 J jnl
Tools for the automatic identification and classification of RNA base pairs.
Nucleic Acids Res.
Huanwang Yang, Fabrice Jossinet, Neocles Leontis, Li Chen, John D. Westbrook, Helen M. Berman, Eric Westhof
2002 J jnl
The Protein Data Bank: unifying the archive.
Nucleic Acids Res.
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
2001 J jnl
The PDB data uniformity project.
Nucleic Acids Res.
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
2000 J jnl
The Protein Data Bank.
Nucleic Acids Res.
Helen M. Berman, John D. Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne
1980 J jnl
The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments.
Nucleic Acids Res.
H. S. Shieh, Helen M. Berman, M. Dabrow, Stephen Neidle