List of works - John Westbrook

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

scientific article published on 18 August 2017

A biologist's guide to synchrotron facilities: the BioSync web resource

scientific article

A framework for scientific data modeling and automated software development

scientific article

An interactive FORTRAN program for three-dimensional molecular visualization

scholarly article by A.R. Srinivasan et al published July 1992 in Computers & Chemistry

An ontology driven architecture for derived representations of macromolecular structure

scientific article

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

scientific article published on 08 April 2019

Archiving and disseminating integrative structure models

scientific article published on 05 July 2019

Archiving of Integrative Structural Models

scientific article published on 01 January 2018

Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank

scientific article (publication date: October 2004)

Bioinformatic Databases

CIF Applications. XI.A La Mode: a ligand and monomer object data environment. I. Automated construction of mmCIF monomer and ligand models

Chemical annotation of small and peptide-like molecules at the Protein Data Bank

scientific article

Contemporary evolution of a Lepidopteran species, Heliothis virescens, in response to modern agricultural practices

scientific article published on 13 November 2017

Correction: Fall armyworm migration across the Lesser Antilles and the potential for genetic exchanges between North and South American populations

scientific article published on 28 March 2017

Crystal, molecular, and electronic structures of pentaammineruthenium(III)-thioether complexes

scientific article published in 1989

Crystallography and Databases

scholarly article by Ian J. Bruno et al published 7 August 2017 in Data Science Journal

DCC: a Swiss army knife for structure factor analysis and validation

scientific article

Data management challenges in three-dimensional EM.

scientific article

Data to knowledge: how to get meaning from your result.

scientific article

Design of a data model for developing laboratory information management and analysis systems for protein production

scientific article

Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules

scientific article published on 9 April 2018

EMDataBank unified data resource for 3DEM.

scientific article

EMDataBank.org: unified data resource for CryoEM

scientific article

Emotional Awareness Moderates the Relationship Between Childhood Abuse and Borderline Personality Disorder Symptom Factors

scientific article published on 4 October 2016

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank

Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic

scientific article published on 04 December 2020

Extension of the sasCIF format and its applications for data processing and deposition

scientific article

Fall armyworm migration across the Lesser Antilles and the potential for genetic exchanges between North and South American populations

scientific article

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

scientific article published on 25 November 2019

Geometric Parameters in Nucleic Acids: Nitrogenous Bases

article

Gossypolhemiquinone, a dimeric sesquiterpenoid identified in cotton (Gossypium).

scientific article published on 22 December 2015

How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals

scientific article published on 27 December 2018

How to use the PSI Structural Genomics Knowledgebase to Enable Research

Impact of the Protein Data Bank on antineoplastic approvals

scientific article published on 14 February 2020

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank

scientific article

Indole RSK inhibitors. Part 1: Discovery and initial SAR ⬇️

scientific article published on October 14, 2011

Ligand Depot: a data warehouse for ligands bound to macromolecules

scientific article

Molecular and electronic structure of (L-histidinato)pentammineruthenium(III) chloride monohydrate, (H3N)5RuIII(his)Cl3·H2O. X-ray structure, single-crystal polarized charge-transfer spectra, and ab initio and semiempirical molecular orbital calcula

article published in 1987

Molecular and electronic structures of pentaammineruthenium(II)-thioether complexes. The nature of Ru(II)-S back bonding elucidated by structural, electronic spectral, and molecular orbital studies

scientific article published in 1992

Molecular electrostatic potentials and partial atomic charges from correlated wave functions: Applications to the electronic ground and excited states of 3-methylindole

Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive

scientific article

NMR Exchange Format: a unified and open standard for representation of NMR restraint data

scientific article

Nucleic acid crystallography: a view from the nucleic acid database.

scientific article published on January 1996

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

scientific article (publication date: March 2017)

Ontologies for three-dimensional molecular structure

Organoiodinane reagents for phosphate cleavage: experimental and computational studies

article

Outcome of a workshop on applications of protein models in biomedical research

scientific article (publication date: 13 February 2009)

Outcome of a workshop on archiving structural models of biological macromolecules

scientific article

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

scientific article published on 18 June 2015

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

scientific article

Outcome of the first electron microscopy validation task force meeting

scientific article (publication date: 8 February 2012)

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

scientific article published in 2024

PDBML: the representation of archival macromolecular structure data in XML.

scientific article

RCSB Protein Data Bank 1D Tools and Services

scientific article published on 12 December 2020

RCSB Protein Data Bank: Architectural advances towards integrated searching and efficient access to macromolecular structure data from the PDB archive

scientific article published on 10 November 2020

RCSB Protein Data Bank: Enabling biomedical research and drug discovery

scientific article published on 29 November 2019

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

scientific article published on 25 October 2017

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

article

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

scientific article published on 19 November 2020

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

scientific article

RNAML: a standard syntax for exchanging RNA information.

scientific article

Realism about PDB.

scientific article

Remediation of the protein data bank archive

scientific article

Report of the working group on crystal phase identifiers

scientific article published on 22 October 2005

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

scientific article

Representation of viruses in the remediated PDB archive

scientific article

Simple models for solvation effects on electronic transition energies: Formaldehyde and water

Simulation of photophysical processes of indoles in solution

Solid-state changes in ligand-to-metal charge-transfer spectra of (NH3)5Ru(III)(2,4-dihydroxybenzoate) and (NH3)5Ru(III)(xanthine) chromophores

scientific article published on 7 October 2008

Solvent effects on the adiabatic free energy difference between the ground and excited states of methylindole in water

Specification of the Crystallographic Information File format, version 2.0

Synthesis and properties of the valence tautomer of cis-iodosocyclopropanecarboxylic acid: 4,5-methano-1-hydroxyiodoxol-3(1H)-one

article

TargetDB: a target registration database for structural genomics projects

scientific article published on 06 May 2004

The CCPN project: an interim report on a data model for the NMR community

scientific article

The Nucleic Acid Database

article from 2002

The Nucleic Acid Database: A resource for nucleic acid science

scientific article published in November 1998

The Nucleic Acid Database: Present and Future

scientific article published on May 1996

The Nucleic Acid Database: new features and capabilities

scientific article published on 31 October 2013

The PDB Format, mmCIF Formats, and Other Data Formats

The PDB format, mmCIF, and other data formats

scientific article

The Protein Data Bank

scientific article (publication date: June 2002)

The Protein Data Bank

The Protein Data Bank and lessons in data management

scientific article

The Protein Data Bank and structural genomics

scientific article

The Protein Data Bank: A Case Study in Management of Community Data

article by Helen M. Berman et al published 1 January 2004 in Current Proteomics: the journal for current and in-depth reviews on proteomics

The Protein Data Bank: unifying the archive

scientific article

The Protein Model Portal

scientific article

The RCSB PDB information portal for structural genomics

scientific article

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

scientific article

The RCSB Protein Data Bank: new resources for research and education

scientific article (publication date: 2013)

The RCSB Protein Data Bank: redesigned web site and web services

scientific article

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

scientific article

The RCSB protein data bank: integrative view of protein, gene and 3D structural information

scientific article

The Structural Biology Knowledgebase - search Online for Protein Sequences, Structures, Functions, Methods and More

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

scientific article

The TRUST Principles for digital repositories

scientific article published on 14 May 2020

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

scientific article

The distribution and query systems of the RCSB Protein Data Bank

scientific article

The evolution of the RCSB Protein Data Bank website

The impact of structural genomics on the protein data bank

scientific article

The need for dictionaries, ontologies, and controlled vocabularies

scientific article published on January 2003

The nucleic acid database

scientific article

The protein structure initiative structural genomics knowledgebase.

scientific article

Tools for the automatic identification and classification of RNA base pairs

scientific article

Validation of Structures in the Protein Data Bank

scientific article published on 21 November 2017

Validation of protein structures for protein data bank

scientific article

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

scientific article published on 7 February 2018

[30] Macromolecular crystallographic information file

article

List of works by John Westbrook

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

A biologist's guide to synchrotron facilities: the BioSync web resource

A framework for scientific data modeling and automated software development

An interactive FORTRAN program for three-dimensional molecular visualization

An ontology driven architecture for derived representations of macromolecular structure

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Archiving and disseminating integrative structure models

Archiving of Integrative Structural Models

Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank

Bioinformatic Databases

CIF Applications. XI.A La Mode: a ligand and monomer object data environment. I. Automated construction of mmCIF monomer and ligand models

Chemical annotation of small and peptide-like molecules at the Protein Data Bank

Contemporary evolution of a Lepidopteran species, Heliothis virescens, in response to modern agricultural practices

Correction: Fall armyworm migration across the Lesser Antilles and the potential for genetic exchanges between North and South American populations

Crystal, molecular, and electronic structures of pentaammineruthenium(III)-thioether complexes

Crystallography and Databases

DCC: a Swiss army knife for structure factor analysis and validation

Data management challenges in three-dimensional EM.

Data to knowledge: how to get meaning from your result.

Design of a data model for developing laboratory information management and analysis systems for protein production

Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules

EMDataBank unified data resource for 3DEM.

EMDataBank.org: unified data resource for CryoEM

Emotional Awareness Moderates the Relationship Between Childhood Abuse and Borderline Personality Disorder Symptom Factors

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank

Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic

Extension of the sasCIF format and its applications for data processing and deposition

Fall armyworm migration across the Lesser Antilles and the potential for genetic exchanges between North and South American populations

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Geometric Parameters in Nucleic Acids: Nitrogenous Bases

Gossypolhemiquinone, a dimeric sesquiterpenoid identified in cotton (Gossypium).

How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals

How to use the PSI Structural Genomics Knowledgebase to Enable Research

Impact of the Protein Data Bank on antineoplastic approvals

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank

Indole RSK inhibitors. Part 1: Discovery and initial SAR ⬇️

Ligand Depot: a data warehouse for ligands bound to macromolecules

Molecular and electronic structure of (L-histidinato)pentammineruthenium(III) chloride monohydrate, (H3N)5RuIII(his)Cl3·H2O. X-ray structure, single-crystal polarized charge-transfer spectra, and ab initio and semiempirical molecular orbital calcula

Molecular and electronic structures of pentaammineruthenium(II)-thioether complexes. The nature of Ru(II)-S back bonding elucidated by structural, electronic spectral, and molecular orbital studies

Molecular electrostatic potentials and partial atomic charges from correlated wave functions: Applications to the electronic ground and excited states of 3-methylindole

Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive

NMR Exchange Format: a unified and open standard for representation of NMR restraint data

Nucleic acid crystallography: a view from the nucleic acid database.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Ontologies for three-dimensional molecular structure

Organoiodinane reagents for phosphate cleavage: experimental and computational studies

Outcome of a workshop on applications of protein models in biomedical research

Outcome of a workshop on archiving structural models of biological macromolecules

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

Outcome of the first electron microscopy validation task force meeting

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

PDBML: the representation of archival macromolecular structure data in XML.

RCSB Protein Data Bank 1D Tools and Services

RCSB Protein Data Bank: Architectural advances towards integrated searching and efficient access to macromolecular structure data from the PDB archive

RCSB Protein Data Bank: Enabling biomedical research and drug discovery

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

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

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

RNAML: a standard syntax for exchanging RNA information.

Realism about PDB.

Remediation of the protein data bank archive

Report of the working group on crystal phase identifiers

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

Representation of viruses in the remediated PDB archive

Simple models for solvation effects on electronic transition energies: Formaldehyde and water

Simulation of photophysical processes of indoles in solution

Solid-state changes in ligand-to-metal charge-transfer spectra of (NH3)5Ru(III)(2,4-dihydroxybenzoate) and (NH3)5Ru(III)(xanthine) chromophores

Solvent effects on the adiabatic free energy difference between the ground and excited states of methylindole in water

Specification of the Crystallographic Information File format, version 2.0

Synthesis and properties of the valence tautomer of cis-iodosocyclopropanecarboxylic acid: 4,5-methano-1-hydroxyiodoxol-3(1H)-one

TargetDB: a target registration database for structural genomics projects

The CCPN project: an interim report on a data model for the NMR community

The Nucleic Acid Database

The Nucleic Acid Database

The Nucleic Acid Database: A resource for nucleic acid science

The Nucleic Acid Database: Present and Future

The Nucleic Acid Database: new features and capabilities