Publications by authors named "Helen Berman"

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IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank.
Arthur O Zalevsky, Brinda Vallat, Benjamin M Webb, Hongsuda Tangmunarunkit, Monica R Sekharan, Helen M Berman

J Mol Biol· December 2025

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RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models.
Brinda Vallat, Yana Rose, Dennis W Piehl, Jose M Duarte, Sebastian Bittrich, Helen M Berman

Nucleic Acids Res· November 2025

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PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures.
Brinda Vallat, Benjamin M Webb, Arthur Zalevsky, Hongsuda Tangmunarunkit, Monica R Sekharan, Helen M Berman

J Mol Biol· August 2025

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Protein Data Bank (PDB): Fifty-three years young and having a transformative impact on science and society.
Helen M Berman, Stephen K Burley

Q Rev Biophys· February 2025

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RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions.
Raktim Mitra, Ari S Cohen, Wei Yu Tang, Hirad Hosseini, Yongchan Hong, Helen M Berman

J Mol Biol· February 2025

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DNAproDB: an updated database for the automated and interactive analysis of protein-DNA complexes.
Raktim Mitra, Ari S Cohen, Jared M Sagendorf, Helen M Berman, Remo Rohs

Nucleic Acids Res· January 2025

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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, Helen M Berman

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, Helen M Berman

J Mol Biol· September 2024

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Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiří Černý, Helen M Berman

Nat Methods· July 2024

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Structural highlights of macromolecular complexes and assemblies.
Brinda Vallat, Helen M Berman

Curr Opin Struct Biol· April 2024

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The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.
Catherine L Lawson, Helen M Berman, Li Chen, Brinda Vallat, Craig L Zirbel

Nucleic Acids Res· January 2024

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Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge.
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiří Černý, Helen M Berman

Res Sq· January 2024

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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, Helen M Berman

J Mol Biol· July 2023

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Crystallographic legacy of Ned Seeman.
Helen M Berman, George DeTitta

Biophys J· 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

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

Biomolecules· October 2022

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More than forty years of nucleic acid structural science.
Gary N Parkinson, Helen Berman

Bioorg Med Chem· September 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, Helen M Berman

J Mol Biol· June 2022

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A new visual design language for biological structures in a cell.
Jitin Singla, Kylie Burdsall, Brian Cantrell, Jordan R Halsey, Alex McDowell, Helen M Berman

Structure· April 2022

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Developing Community Resources for Nucleic Acid Structures.
Helen M Berman, Catherine L Lawson, Bohdan Schneider

Life (Basel)· April 2022

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New system for archiving integrative structures.
Brinda Vallat, Benjamin Webb, Maryam Fayazi, Serban Voinea, Hongsuda Tangmunarunkit, Helen M Berman

Acta Crystallogr D Struct Biol· December 2021

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How the Protein Data Bank changed biology: An introduction to the JBC Reviews thematic series, part 1.
Helen M Berman, Lila M Gierasch

J Biol Chem· August 2021

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How the Protein Data Bank changed biology: An introduction to the JBC Reviews thematic series, part 2.
Lila M Gierasch, Helen M Berman

J Biol Chem· August 2021

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Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction.
Stephen K Burley, Helen M Berman

Structure· June 2021

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Synergies between the Protein Data Bank and the community.
Helen M Berman

Nat Struct Mol Biol· May 2021

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