John D. Westbrook

Publication Activity (10 Years)

Years Active: 1992-2024
Publications (10 Years): 12

Top Topics

Scientific Disciplines

Protein Data Bank

Structural Information

Top Venues

Nucleic Acids Res.

Database J. Biol. Databases Curation

Publications

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
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank. Database J. Biol. Databases Curation 2024 (2024)
John D. Westbrook, Diane Jakacki, Rebecca Heintzelman, Juliya Harnood
Digitizing Suzette: Creating a Framework for the Collaborative Analysis of an Historical French Textbook. DH (2023)
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
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. 51 (D1) (2023)
Sebastian Bittrich, Yana Rose, Joan Segura, Robert Lowe, John D. Westbrook, Jose M. Duarte, Stephen K. Burley
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB. Bioinform. 38 (5) (2022)
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
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. 49 (Database-Issue) (2021)
Joan Segura, Yana Rose, John D. Westbrook, Stephen K. Burley, Jose M. Duarte
RCSB Protein Data Bank 1D tools and services. Bioinform. 36 (22-23) (2021)
Zukang Feng, Natalie Verdiguel, Luigi Di Costanzo, David S. Goodsell, John D. Westbrook, Stephen K. Burley, Christine Zardecki
Impact of the Protein Data Bank Across Scientific Disciplines. Data Sci. J. 19 (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)
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)
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)
Ian J. Bruno, Saulius Grazulis, John R. Helliwell, Soorya N. Kabekkodu, Brian McMahon, John D. Westbrook
Crystallography and Databases. Data Sci. J. 16 (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)
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)
John D. Westbrook, Chenghua Shao, Zukang Feng, Marina Zhuravleva, Sameer Velankar, Jasmine Young
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. Bioinform. 31 (8) (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)
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)
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)
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)
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)
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
A framework for scientific data modeling and automated software development. Bioinform. 21 (8) (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)
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
The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures. Pacific Symposium on Biocomputing (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)
Douglas S. Greer, John D. Westbrook, Philip E. Bourne
An ontology driven architecture for derived representations of macromolecular structure. Bioinform. 18 (9) (2002)
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)
John D. Westbrook, Philip E. Bourne
STAR/mmCIF: An ontology for macromolecular structure. Bioinform. 16 (2) (2000)
Annankoil R. Srinivasan, John D. Westbrook, Wilma K. Olson
An Interactive FORTRAN Program for Three-dimensional Molecular Visualization. Comput. Chem. 16 (3) (1992)