Explanipedia

RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models Open

Brinda Vallat, Yana Rose, Dennis W. Piehl, José M. Duarte, Sebastian Bittrich , et al. · 2025

The Protein Data Bank (PDB) archives 3D structures of macromolecules determined experimentally using various methods. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) consortium. Research Collaboratory for Structural Bioinf…

Streamlining OneDep Depositions of Multiple Related 3DEM Entries with pdb_extract Open

Justin W. Flatt, Chenghua Shao, Brian P. Hudson, Irina Persikova, Yu‐He Liang , et al. · 2025

The Protein Data Bank (PDB) was established in 1971 as the first open-access digital resource in biology with just seven deposited protein structures. Today, the single global PDB archive houses more than 233,000 experimentally determined …

Data Archive Challenge: Transitioning Users to New IDs and Data File Format at the Protein Data Bank Open

Brian P. Hudson, Zukang Feng, Irina Persikova, Yu‐He Liang, Ezra Peisach , et al. · 2025

The Protein Data Bank (PDB), established in 1971 as the first open-access digital resource in biology, has grown from seven X-ray crystallographic structures to over 233,000 3D structures of biological macromolecules supporting research an…

Improving Data Representation of Metalloproteins in the Protein Data Bank Open

Alison Biester, Chenghua Shao, Zukang Feng, Ezra Peisach, Jasmine Young , et al. · 2025

The Protein Data Bank (PDB) was established in 1971 as the first open-access digital data resource in biology, initially comprising just seven X- ray crystal structures of proteins. Today, the archive houses more than 225,000 experimentall…

Sixth Decade of Protein Data Bank Operations: Transition to Extended PDB IDs and PDBx/mmCIF Format Open

Sutapa Ghosh, Zukang Feng, Yu‐He Liang, Ezra Peisach, Irina Persikova , et al. · 2025

The Protein Data Bank (PDB) was established in 1971 as the first open-access digital data resource in biology with just seven X-ray crystallographic structures of proteins. Today, the single global PDB archive houses more than 215,000 expe…

IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank Open

Arthur O. Zalevsky, Brinda Vallat, Benjamin Webb, Hongsuda Tangmunarunkit, Monica Sekharan , et al. · 2025

Transitioning to new PDB IDs and PDBx/mmCIF format at the Protein Data Bank Open

Jasmine Young · 2025

Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit Open

Sebastian Bittrich, Adam Midlik, Mihály Váradi, Sameer Velankar, S.K. Burley , et al. · 2024

With the ever‐expanding toolkit of molecular viewers, the ability to visualize macromolecular structures has never been more accessible. Yet, the idiosyncratic technical intricacies across tools and the integration complexities associated …

Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank Open

Kumaran Baskaran, Eliza Płoskoń, Roberto Tejero, Masashi Yokochi, Déborah Harrus , et al. · 2024

Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards…

Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank Open

Kumaran Baskaran, Eliza Płoskoń, Roberto Tejero, Masashi Yokochi, Déborah Harrus , et al. · 2024

Summary Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of s…

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

Preeti Choudhary, Zukang Feng, John M. Berrisford, Henry Chao, Yasuyo Ikegawa , et al. · 2024

The Protein Data Bank (PDB) is the global repository for public-domain experimentally determined 3D biomolecular structural information. The archival nature of the PDB presents certain challenges pertaining to updating or adding associated…

PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank Open

Preeti Choudhary, Zukang Feng, John M. Berrisford, Henry Chao, Yasuyo Ikegawa , et al. · 2023

The Protein Data Bank (PDB) archive is the global repository for public-domain 3D biomolecular structural information. The archival nature of the PDB presents certain challenges pertaining to updating or adding associated annotations from …

Assessing and Maximizing the Quality of 3DEM Structure Data at the Worldwide Protein Data Bank Open

Justin W. Flatt, Brian P. Hudson, Irina Persikova, Yu‐He Liang, Chenghua Shao , et al. · 2023

Journal Article Assessing and Maximizing the Quality of 3DEM Structure Data at the Worldwide Protein Data Bank Get access Justin W Flatt, Justin W Flatt RCSB Protein Data Bank, Rutgers, The State University of New Jersey, New Jersey, Unite…

Restraint Validation of Biomolecular Structures Determined By NMR in the Protein Data Bank Open

Kumaran Baskaran, Eliza Płoskoń, Roberto Tejero, Masashi Yokochi, Déborah Harrus , et al. · 2023

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology Open

John D. Westbrook, Jasmine Young, Chenghua Shao, Zukang Feng, Vladimir Guranović , et al. · 2022

The next generation RCSB.org Open

Justin W. Flatt, José M. Duarte, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich , et al. · 2021

The life and times of the PDB format – looking towards the future with mmCIF Open

G.V. Crichlow, C. W. Lawson, John D. Westbrook, S.K. Burley, Sanja Abbott , et al. · 2021

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

Zukang Feng, John D. Westbrook, Raul Sala, Oliver S. Smart, G. Bricogne , et al. · 2021

Enabling depositor-initiated PDB coordinate replacement through file versioning Open

Christine Zardecki, Jasmine Young, John D. Westbrook, Zukang Feng, Ezra Peisach , et al. · 2019

Enabling findability, accessibility, interoperability, and reusability with improved data representation of carbohydrates in the Protein Data Bank Open

Jasmine Young, Chenghua Shao, Zukang Feng, John D. Westbrook, Ezra Peisach , et al. · 2019

Creating and maintaining a data archive for 3D structures of biological macromolecules Open

Jasmine Young, John D. Westbrook, S.K. Burley, wwPDB Consortium · 2019

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

Christine Zardecki, Helen M. Berman, Cole Christie, José M. Duarte, Zukang Feng , et al. · 2018

New online curriculum: the PDB pipeline and data archiving Open

Catherine L. Lawson, Margaret Gabanyi, John D. Westbrook, Jasmine Young, Shuchismita Dutta , et al. · 2018

RCSB Protein Data Bank: enabling breakthroughs in biomedical research and structure-guided drug discovery Open

Christine Zardecki, Chenghua Shao, John D. Westbrook, Zukang Feng, Jasmine Young · 2018

RCSB Protein Data Bank: Sustaining A Living Digital Data Resource That Enables Breakthroughs In Scientific Research And Biomedical Education Open

S.K. Burley, Helen M. Berman, Cole Christie, José M. Duarte, Zukang Feng , et al. · 2018

Protein Data Bank (PDB) was established as the 1st open access digital data resource in biology and medicine. Today, the PDB is one of two global resources for experimental data central to science as a public good (the other key Primary Da…

RCSB PDB: structural biology views for basic and applied research Open

Christine Zardecki, S.K. Burley, Cole Christie, José M. Duarte, Zukang Feng , et al. · 2017

tools for structure query, analysis, and visualization (Berman et al., 2000; Rose et al., 2017).Users can perform simple searches from the top search bar (e.g., ID, name, sequence, ligand) or build complex combinations of search parameters…

OneDep: unified wwPDB system for deposition, biocuration and validation of macromolecular structures in the PDB archive Open

Jasmine Young, John D. Westbrook, Zukang Feng, wwPDB Team, wwPDB Onedep Team , et al. · 2017

Multivariate analyses of quality metrics for crystal structures in the PDB archive Open

Chenghua Shao, Huanwang Yang, John D. Westbrook, Jasmine Young, Christine Zardecki , et al. · 2017

Following deployment of an augmented validation system by the Worldwide Protein Data Bank (wwPDB) partnership, the quality of crystal structures entering the PDB has improved. Of significance are improvements in quality measures now promin…

Biocuration of experimentally-determined 3D macromolecular structures and their complexes at the wwPDB Open

Jasmine Young, John M. Berrisford, Reiko Igarashi, wwPDB Biocuration Team, wwPDV OneDep Team , et al. · 2017

<i>DCC</i>: a Swiss army knife for structure factor analysis and validation Open

Huanwang Yang, Ezra Peisach, John D. Westbrook, Jasmine Young, Helen M. Berman , et al. · 2016

Since 2008, X-ray structure depositions to the Protein Data Bank archive (PDB) have required submission of experimental data in the form of structure factor files. RCSB PDB has developed the program DCC to allow worldwide PDB (wwPDB; http:…

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