John D. Westbrook

40 papers Misc 1Journal 37Unranked 1
YearRankTypeTitle / Venue / Authors
2024 J jnl
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.
Database J. Biol. Databases Curation
Preeti Choudhary, Zukang Feng, John M. Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D. Westbrook, Jasmine Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley
2023 — conf
Digitizing Suzette: Creating a Framework for the Collaborative Analysis of an Historical French Textbook.
DH
John D. Westbrook, Diane Jakacki, Rebecca Heintzelman, Juliya Harnood
2023 J jnl
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.
Nucleic Acids Res.
Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Henry Chao, Li Chen, Paul A. Craig, Gregg V. Crichlow, Kenneth Dalenberg, Jose M. Duarte, Shuchismita Dutta, Maryam Fayazi, Zukang Feng, Justin W. Flatt, Sai Ganesan, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Jeremy Henry, Brian P. Hudson, Igor Khokhriakov, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Ezra Peisach, Irina Persikova, Dennis W. Piehl, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, Ben M. Webb, John D. Westbrook, Shamara Whetstone, Jasmine Young, Arthur O. Zalevsky, Christine Zardecki
2022 J jnl
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB.
Bioinform.
Sebastian Bittrich, Yana Rose, Joan Segura, Robert Lowe, John D. Westbrook, Jose M. Duarte, Stephen K. Burley
2021 J jnl
RCSB Protein Data Bank 1D tools and services.
Bioinform.
Joan Segura, Yana Rose, John D. Westbrook, Stephen K. Burley, Jose M. Duarte
2021 J jnl
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.
Nucleic Acids Res.
Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V. Crichlow, Cole H. Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sai Ganesan, David S. Goodsell, Sutapa Ghosh, Rachel Kramer Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Persikova, Christopher Randle, Alexander S. Rose, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Yi-Ping Tao, Maria Voigt, John D. Westbrook, Jasmine Young, Christine Zardecki, Marina Zhuravleva
2020 J jnl
Impact of the Protein Data Bank Across Scientific Disciplines.
Data Sci. J.
Zukang Feng, Natalie Verdiguel, Luigi Di Costanzo, David S. Goodsell, John D. Westbrook, Stephen K. Burley, Christine Zardecki
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
Crystallography and Databases.
Data Sci. J.
Ian J. Bruno, Saulius Grazulis, John R. Helliwell, Soorya N. Kabekkodu, Brian McMahon, John D. Westbrook
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
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
2015 J jnl
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.
Bioinform.
John D. Westbrook, Chenghua Shao, Zukang Feng, Marina Zhuravleva, Sameer Velankar, Jasmine Young
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
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
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
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 — ch.
Bioinformatic Databases.
Wiley Encyclopedia of Computer Science and Engineering
Katherine G. Herbert, Junilda Spirollari, Jason Tsong-Li Wang, William H. Piel, John D. Westbrook, Winona C. Barker, Zhang-Zhi Hu, Cathy H. Wu
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
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
A framework for scientific data modeling and automated software development.
Bioinform.
Rasmus H. Fogh, Wayne Boucher, Wim F. Vranken, Anne Pajon, Tim J. Stevens, T. N. Bhat, John D. Westbrook, John M. C. Ionides, Ernest D. Laue
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 Misc conf
The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures.
Pacific Symposium on Biocomputing
Philip E. Bourne, C. K. J. Allerston, Werner G. Krebs, Wilfred W. Li, Ilya N. Shindyalov, Adam Godzik, Iddo Friedberg, Tong Liu, David L. Wild, Seungwoo Hwang, Zoubin Ghahramani, Li Chen, John D. Westbrook
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
An ontology driven architecture for derived representations of macromolecular structure.
Bioinform.
Douglas S. Greer, John D. Westbrook, Philip E. Bourne
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
STAR/mmCIF: An ontology for macromolecular structure.
Bioinform.
John D. Westbrook, Philip E. Bourne
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
1992 J jnl
An Interactive FORTRAN Program for Three-dimensional Molecular Visualization.
Comput. Chem.
Annankoil R. Srinivasan, John D. Westbrook, Wilma K. Olson