List of works - Helen M. Berman

27 Analysis of DNA deformations in transcription factor-DNA complexes

scientific article published in May 2015

A crystallographic determination of a chemical structure: 6-amino-10-(beta-D-ribofuranosylamino)pyrimido-[5,4-d]pyrimidine, an example of an unusual D-ribose conformation

scientific article published on November 1, 1975

A molecular model for proflavine-DNA intercalation

scientific article published on September 1988

A second determination of the structure of hydroxyurea

scientific article

A structural model for sequence-specific proflavin-DNA interactions during in vitro frameshift mutagenesis

scientific article published on October 1, 1992

A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction

scientific article

A systematic method for studying the spatial distribution of water molecules around nucleic acid bases

scientific article

An analysis of the relationship between hydration and protein-DNA interactions

scientific article

An improved basal medium for Y-1 mouse adrenal cortex tumor cells in culture. 2. Stability of steroidogenic pathway and chromosome number

scientific article published on July 1981

An improved, reproducible method opreparing rat liver plasma cell membranes in buffered isotonic sucrose

scientific article

An overview of the structures of protein-DNA complexes

scientific article

Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes

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

Announcing the worldwide Protein Data Bank

scientific article (publication date: December 2003)

Anomeric Bond-Character in the Pyranose Sugars ⬇️

scientific article

Anticipating innovations in structural biology

scientific article published on 01 January 2018

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

Aromatic hydrogen bond in sequence-specific protein DNA recognition

scientific article

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

scientific article (publication date: October 2004)

BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

scientific article

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

Catabolite activator protein: DNA binding and transcription activation

scientific article

Cellular swelling. II. Effects of hypotonicity, low molecular weight dextran addition and pH changes on oxygen consumption of isolated tissues

scientific article published in April 1966

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

scientific article

Comment on on the propagation of errors by Jaskolski (2013).

scientific article published on 19 November 2013

Comment on timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013).

scientific article published on 19 November 2013

Conformational effects of Gly-X-Gly interruptions in the collagen triple helix

scientific article

Creating a community resource for protein science ⬇️

scientific article published on September 28, 2012

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

scientific article published on 04 February 2021

Crystal and Molecular Structure of a Collagen-Like Peptide at 1.9 Å Resolution ⬇️

scientific article published on October 7, 1994

Crystal and molecular structure of a DNA duplex containing the carcinogenic lesion O6-methylguanine

scientific article

Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers

scientific article

Crystal and molecular structure of a DNA fragment: d(CGTGAATTCACG)

scientific article

Crystal and molecular structure of a new Z-DNA crystal form: d[CGT(2-NH2-A)CG] and its platinated derivative

scientific article

Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction

scientific article

Crystal structure of a mispaired dodecamer, d(CGAGAATTC(O6Me)GCG)2, containing a carcinogenic O6-methylguanine

scientific article

Crystal structure of a naturally occurring dinucleoside phosphate: Uridylyl 3′,5′-adenosine phosphate model for RNA chain folding ⬇️

scientific article published on May 28, 1972

Crystal structure of the unique RNA-binding domain of the influenza virus NS1 protein ⬇️

scientific article published on November 1, 1997

Crystallization, X-ray studies, and site-directed cysteine mutagenesis of the DNA-binding domain of OmpR.

scientific article published on July 1996

Cuba's free medical education for US students

scientific article

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

scientific article

DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes

scientific article published on 01 January 2020

DNAproDB: an interactive tool for structural analysis of DNA-protein complexes

scientific article published on 20 April 2017

Data Deposition and Annotation at the Worldwide Protein Data Bank

article by Shuchismita Dutta et al published 10 December 2008 in Molecular Biotechnology

Data deposition and annotation at the worldwide protein data bank

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

Doppler diagnosis of subclavian steal due to arteriovenous hemodialysis fistula in the ipsilateral arm.

scientific article published in December 1989

E. coli trp repressor forms a domain-swapped array in aqueous alcohol

scientific article published on June 2004

EMDataBank unified data resource for 3DEM.

scientific article

EMDataBank.org: unified data resource for CryoEM

scientific article

Emdatabank: Unified Data Resource for 3DEM

Evolving data standards for cryo-EM structures

scientific article published on 24 January 2020

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

scientific article published on 25 November 2019

Fundamentals of DNA and RNA structure.

scientific article

Future structural genomics initiatives: an interview with Helen Berman, director of the Protein Data Bank. Interview by Wendy A Warr

scientific article published on 10 September 2008

Geometric Parameters in Nucleic Acids: Nitrogenous Bases

article

Harnessing knowledge from structural genomics

scientific article

How community has shaped the Protein Data Bank

scientific article

How to use the PSI Structural Genomics Knowledgebase to Enable Research

Hydration of DNA bases: analysis of crystallographic data

scientific article published on July 1, 1992

Hydration of the DNA bases is local

scientific article

Hydration of the phosphate group in double-helical DNA

scientific article

Hydration structure of a collagen peptide

scientific article

Hydrogen bonding in biological structures. G. A. Jeffrey and W. Saenger

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

scientific article

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking

scientific article

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking

scientific article

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps

scientific article

Insights from 20 years of the Molecule of the Month

scientific article published on 17 June 2020

Knowledge-based generation of machine learning experiments: learning with DNA crystallography data

scientific article published on January 1, 1993

Large macromolecular complexes in the Protein Data Bank: a status report

scientific article

Ligand Depot: a data warehouse for ligands bound to macromolecules

scientific article

Low temperature structures of dCpG-proflavine. Conformational and hydration effects

scientific article

Magnetic resonance imaging of dissection in pseudocoarctation of the aorta

scientific article published in May 1993

Metabolic syndrome in Argentinean patients with systemic lupus erythematosus

scientific article published on 21 December 2009

Metabolism of rat granular pneumocytes isolated in primary culture

scientific article published in October 1980

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

scientific article

Netropsin, a DNA-binding oligopeptide structural and binding studies ⬇️

scientific article published on January 26, 1979

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

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-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

scientific article

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

scientific article

PROTEIN NUCLEIC ACID INTERACTIONS GRANT # DE-FG02-96ER62166 FINAL REPORT

Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences

scientific article (publication date: October 2010)

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive

scientific article

Protein structure annotation resources.

scientific article

Protein-RNA interactions: a structural analysis

scientific article

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank

scientific article

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank

scientific article

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

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

scientific article

RNA conformational classes

scientific article published on 11 March 2004

Realism about PDB.

scientific article

Recommendations of the wwPDB NMR Validation Task Force

scientific article

Remediation of the protein data bank archive

scientific article

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

Response to On prompt update of literature references in the Protein Data Bank

scientific article published on 30 September 2014

Revealing structural views of biology

scientific article

Safeguarding the integrity of protein archive

scientific article published on January 2010

Sequence dependent conformational variations of collagen triple-helical structure

scientific article

Signatures of Protein-DNA Recognition in Free DNA Binding Sites

scientific article

Staggered molecular packing in crystals of a collagen-like peptide with a single charged pair

scientific article

Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif

scientific article

Structural basis of transcription activation: the CAP-alpha CTD-DNA complex

scientific article

Structure of a dinucleoside phosphate--drug complex as model for nucleic acid--drug interaction

scientific article published in September 1977

Structure of a new crystal form of a DNA dodecamer containing T.(O6Me)G base pairs

scientific article

Structure of an interleukin-1 beta mutant with reduced bioactivity shows multiple subtle changes in conformation that affect protein-protein recognition

scientific article

Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface

scientific article

TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES

scientific article (publication date: 23 February 2017)

Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction

scientific article

TargetDB: a target registration database for structural genomics projects

scientific article published on 06 May 2004

The 2010 cryo-EM modeling challenge

scientific article published in September 2012

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: 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 data uniformity project

scientific article

The Protein Data Bank

scientific article

The Protein Data Bank

scientific article (publication date: June 2002)

The Protein Data Bank and lessons in data management

scientific article

The Protein Data Bank and structural genomics

scientific article

The Protein Data Bank archive as an open data resource

scientific article

The Protein Data Bank at 40: reflecting on the past to prepare for the future

scientific article (publication date: 7 March 2012)

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: Overview and Tools for Drug Discovery

The Protein Data Bank: a historical perspective

scientific article published on 21 December 2007

The Protein Data Bank: unifying the archive

scientific article

The Protein Model Portal

scientific article

The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource

scientific article

The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology

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 RNA Ontology Consortium: an open invitation to the RNA community

scientific article published on 16 February 2006

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 archiving and dissemination of biological structure data

scientific article

The cAMP binding domain: an ancient signaling module

scientific article

The crystal structure of a uracil-acetone photoaddition product ⬇️

scientific article published on November 4, 1975

The crystal structure of an autoprocessed Ser221Cys-subtilisin E-propeptide complex at 2.0 A resolution

scientific article

The data universe of structural biology

scientific article published on 28 May 2020

The distribution and query systems of the RCSB Protein Data Bank

scientific article

The evolution of the RCSB Protein Data Bank website

The future of the Protein Data Bank

scientific article (publication date: March 2013)

The impact of structural genomics on the protein data bank

scientific article

The interaction of intercalating drugs with nucleic acids

scientific article published on January 1981

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

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

scientific article

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

scientific article

Tools for the automatic identification and classification of RNA base pairs

scientific article

Trendspotting in the Protein Data Bank

scientific article

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.

scientific article

Using the Tools and Resources of the RCSB Protein Data Bank

Using the tools and resources of the RCSB protein data bank

scientific article published in December 2007

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

Workshop on the validation and modeling of electron cryo-microscopy structures of biological nanomachines

scientific article published on January 2011

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

scientific article published on 7 February 2018

X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly)

scientific article

[30] Macromolecular crystallographic information file

article

List of works by Helen M. Berman

27 Analysis of DNA deformations in transcription factor-DNA complexes

A crystallographic determination of a chemical structure: 6-amino-10-(beta-D-ribofuranosylamino)pyrimido-[5,4-d]pyrimidine, an example of an unusual D-ribose conformation

A molecular model for proflavine-DNA intercalation

A second determination of the structure of hydroxyurea

A structural model for sequence-specific proflavin-DNA interactions during in vitro frameshift mutagenesis

A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction

A systematic method for studying the spatial distribution of water molecules around nucleic acid bases

An analysis of the relationship between hydration and protein-DNA interactions

An improved basal medium for Y-1 mouse adrenal cortex tumor cells in culture. 2. Stability of steroidogenic pathway and chromosome number

An improved, reproducible method opreparing rat liver plasma cell membranes in buffered isotonic sucrose

An overview of the structures of protein-DNA complexes

Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes

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

Announcing the worldwide Protein Data Bank

Anomeric Bond-Character in the Pyranose Sugars ⬇️

Anticipating innovations in structural biology

Archiving and disseminating integrative structure models

Archiving of Integrative Structural Models

Aromatic hydrogen bond in sequence-specific protein DNA recognition

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

BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

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

Catabolite activator protein: DNA binding and transcription activation

Cellular swelling. II. Effects of hypotonicity, low molecular weight dextran addition and pH changes on oxygen consumption of isolated tissues

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

Comment on on the propagation of errors by Jaskolski (2013).

Comment on timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013).

Conformational effects of Gly-X-Gly interruptions in the collagen triple helix

Creating a community resource for protein science ⬇️

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

Crystal and Molecular Structure of a Collagen-Like Peptide at 1.9 Å Resolution ⬇️

Crystal and molecular structure of a DNA duplex containing the carcinogenic lesion O6-methylguanine

Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers

Crystal and molecular structure of a DNA fragment: d(CGTGAATTCACG)

Crystal and molecular structure of a new Z-DNA crystal form: d[CGT(2-NH2-A)CG] and its platinated derivative

Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction

Crystal structure of a mispaired dodecamer, d(CGAGAATTC(O6Me)GCG)2, containing a carcinogenic O6-methylguanine

Crystal structure of a naturally occurring dinucleoside phosphate: Uridylyl 3′,5′-adenosine phosphate model for RNA chain folding ⬇️

Crystal structure of the unique RNA-binding domain of the influenza virus NS1 protein ⬇️

Crystallization, X-ray studies, and site-directed cysteine mutagenesis of the DNA-binding domain of OmpR.

Cuba's free medical education for US students

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

DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes

DNAproDB: an interactive tool for structural analysis of DNA-protein complexes

Data Deposition and Annotation at the Worldwide Protein Data Bank

Data deposition and annotation at the worldwide protein data bank

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

Doppler diagnosis of subclavian steal due to arteriovenous hemodialysis fistula in the ipsilateral arm.

E. coli trp repressor forms a domain-swapped array in aqueous alcohol

EMDataBank unified data resource for 3DEM.

EMDataBank.org: unified data resource for CryoEM

Emdatabank: Unified Data Resource for 3DEM

Evolving data standards for cryo-EM structures

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

Fundamentals of DNA and RNA structure.

Future structural genomics initiatives: an interview with Helen Berman, director of the Protein Data Bank. Interview by Wendy A Warr

Geometric Parameters in Nucleic Acids: Nitrogenous Bases

Harnessing knowledge from structural genomics

How community has shaped the Protein Data Bank

How to use the PSI Structural Genomics Knowledgebase to Enable Research

Hydration of DNA bases: analysis of crystallographic data

Hydration of the DNA bases is local

Hydration of the phosphate group in double-helical DNA

Hydration structure of a collagen peptide

Hydrogen bonding in biological structures. G. A. Jeffrey and W. Saenger

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

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps

Insights from 20 years of the Molecule of the Month

Knowledge-based generation of machine learning experiments: learning with DNA crystallography data

Large macromolecular complexes in the Protein Data Bank: a status report

Ligand Depot: a data warehouse for ligands bound to macromolecules

Low temperature structures of dCpG-proflavine. Conformational and hydration effects

Magnetic resonance imaging of dissection in pseudocoarctation of the aorta

Metabolic syndrome in Argentinean patients with systemic lupus erythematosus

Metabolism of rat granular pneumocytes isolated in primary culture