Publications by authors named "John D Westbrook"

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Making fluorescence-based integrative structures and associated kinetic information accessible.
Christian A Hanke, John D Westbrook, Benjamin M Webb, Thomas-O Peulen, Catherine L Lawson

Nat Methods· November 2024

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IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.
Brinda Vallat, Benjamin M Webb, John D Westbrook, Thomas D Goddard, Christian A Hanke

J Mol Biol· September 2024

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Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.
Kumaran Baskaran, Eliza Ploskon, Roberto Tejero, Masashi Yokochi, Deborah Harrus, John D Westbrook

Structure· June 2024

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PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.
Preeti Choudhary, Zukang Feng, John Berrisford, Henry Chao, Yasuyo Ikegawa, John D Westbrook

Database (Oxford)· May 2024

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Community recommendations on cryoEM data archiving and validation.
Gerard J Kleywegt, Paul D Adams, Sarah J Butcher, Catherine L Lawson, Alexis Rohou, John D Westbrook

IUCrJ· March 2024

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Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation.
Gerard J Kleywegt, Paul D Adams, Sarah J Butcher, Catherine L Lawson, Alexis Rohou, John D Westbrook

ArXiv· February 2024

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Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank.
Kumaran Baskaran, Eliza Ploskon, Roberto Tejero, Masashi Yokochi, Deborah Harrus, John D Westbrook

bioRxiv· January 2024

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RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances.
Sebastian Bittrich, Charmi Bhikadiya, Chunxiao Bi, Henry Chao, Jose M Duarte, John D Westbrook

J Mol Biol· July 2023

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ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.
Brinda Vallat, Gerardo Tauriello, Stefan Bienert, Juergen Haas, Benjamin M Webb, John D Westbrook

J Mol Biol· July 2023

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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, John D Westbrook

Nucleic Acids Res· January 2023

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RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.
Stephen K Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Henry Chao, John D Westbrook

Protein Sci· December 2022

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Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.
Stephen K Burley, Helen M Berman, Wah Chiu, Wei Dai, Justin W Flatt, John D Westbrook

Biophys Rev· December 2022

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Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.
Stephen K Burley, Helen M Berman, Jose M Duarte, Zukang Feng, Justin W Flatt, John D Westbrook

Biomolecules· October 2022

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PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.
John D Westbrook, Jasmine Y Young, Chenghua Shao, Zukang Feng, Vladimir Guranovic

J Mol Biol· June 2022

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Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic.
Joseph H Lubin, Christine Zardecki, Elliott M Dolan, Changpeng Lu, Zhuofan Shen, John D Westbrook

Proteins· May 2022

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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

Bioinformatics· February 2022

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Simplified quality assessment for small-molecule ligands in the Protein Data Bank.
Chenghua Shao, John D Westbrook, Changpeng Lu, Charmi Bhikadiya, Ezra Peisach

Structure· February 2022

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RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.
Stephen K Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, John D Westbrook

Protein Sci· January 2022

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New system for archiving integrative structures.
Brinda Vallat, Benjamin Webb, Maryam Fayazi, Serban Voinea, Hongsuda Tangmunarunkit, John D Westbrook

Acta Crystallogr D Struct Biol· December 2021

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Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.
Chenghua Shao, Zukang Feng, John D Westbrook, Ezra Peisach, John Berrisford

Glycobiology· September 2021

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Interventions for improving employment outcomes for persons with autism spectrum disorders: A systematic review update.
Carlton J Fong, Joshua Taylor, Aynura Berdyyeva, Amanda M McClelland, Kathleen M Murphy, John D Westbrook

Campbell Syst Rev· September 2021

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RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive.
Yana Rose, Jose M Duarte, Robert Lowe, Joan Segura, Chunxiao Bi, John D Westbrook

J Mol Biol· May 2021

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Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.
Zukang Feng, John D Westbrook, Raul Sala, Oliver S Smart, Gérard Bricogne

Structure· April 2021

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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, John D Westbrook

Nucleic Acids Res· January 2021

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Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic.
Joseph H Lubin, Christine Zardecki, Elliott M Dolan, Changpeng Lu, Zhuofan Shen, John D Westbrook

bioRxiv· December 2020

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