John D. Westbrook

According to our database, John D. Westbrook authored at least 40 papers between 1992 and 2024.

Collaborative distances:

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

2024

PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.

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

Database J. Biol. Databases Curation, January, 2024

2023

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.

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

Nucleic Acids Res., January, 2023

Digitizing Suzette: Creating a Framework for the Collaborative Analysis of an Historical French Textbook.

John D. Westbrook, Diane Jakacki, Rebecca Heintzelman, Juliya Harnood

Proceedings of the Annual International Conference of the Alliance of Digital Humanities Organizations, 2023

2022

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB.

Sebastian Bittrich, Yana Rose, Joan Segura, Robert Lowe, John D. Westbrook, Jose M. Duarte, Stephen K. Burley

Bioinform., 2022

2021

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.

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

Nucleic Acids Res., 2021

RCSB Protein Data Bank 1D tools and services.

Joan Segura, Yana Rose, John D. Westbrook, Stephen K. Burley, Jose M. Duarte

Bioinform., 2021

2020

Impact of the Protein Data Bank Across Scientific Disciplines.

Zukang Feng, Natalie Verdiguel, Luigi Di Costanzo, David S. Goodsell, John D. Westbrook, Stephen K. Burley, Christine Zardecki

Data Sci. J., 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

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

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

Crystallography and Databases.

Ian J. Bruno, Saulius Grazulis, John R. Helliwell, Soorya N. Kabekkodu, Brian McMahon, John D. Westbrook

Data Sci. J., 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

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.

John D. Westbrook, Chenghua Shao, Zukang Feng, Marina Zhuravleva, Sameer Velankar, Jasmine Young

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

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

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

Bioinformatic Databases.

Katherine G. Herbert, Junilda Spirollari, Jason Tsong-Li Wang, William H. Piel, John D. Westbrook, Winona C. Barker, Zhang-Zhi Hu, Cathy H. Wu

Proceedings of the Wiley Encyclopedia of Computer Science and Engineering, 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

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

A framework for scientific data modeling and automated software development.

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

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

The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures.

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

Proceedings of the Biocomputing 2004, 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

An ontology driven architecture for derived representations of macromolecular structure.

Douglas S. Greer, John D. Westbrook, Philip E. Bourne

Bioinform., 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

STAR/mmCIF: An ontology for macromolecular structure.

John D. Westbrook, Philip E. Bourne

Bioinform., 2000

1992

An Interactive FORTRAN Program for Three-dimensional Molecular Visualization.

Annankoil R. Srinivasan, John D. Westbrook, Wilma K. Olson

Comput. Chem., 1992