Chart Builder provides an interactive tool for visualizing and exploring metadata from cryoEM archives, enabling users to create customizable charts and access underlying datasets.

Frontiers in Bioinformatics · Mar 6, 2026Peer-reviewedBiophysics

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

Kumaran Baskaran, Eliza Płoskoń, Roberto Tejero, Masashi Yokochi, Déborah Harrus, Yu‐He Liang, Ezra Peisach, Irina Persikova, Theresa A. Ramelot, Monica R. Sekharan, James L. Tolchard, John Westbrook, Benjamin Bardiaux, Charles D. Schwieters, Ardan Patwardhan, , Jasmine Y. Young

The paper develops a standardized system for validating biomolecular structures against NMR restraints using NEF and NMR-STAR formats, implemented in the wwPDB OneDep system.

Structure · Mar 14, 2024Peer-reviewedBioinformatics

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

Preeti Choudhary, Zukang Feng, John M. Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihály Váradi, John Westbrook, Jasmine Y. Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch, , Stephen Kevin Burley

The PDB NextGen Archive centralizes and streamlines access to integrated structural annotations and enriched data from wwPDB partners and external sources.

Database · Jan 1, 2024Peer-reviewedBioinformatics

EMDB - The Electron Microscopy Data Bank

Jack Turner, Sanja Abbott, Neli Fonseca, Ryan Pye, Lucas Carrijo de Oliveira, Amudha Kumari Duraisamy, Osman Salih, Zhe Wang, Gerard J. Kleywegt, Kyle L. Morris, Ardan Patwardhan, Stephen Kevin Burley, G.V. Crichlow, Zukang Feng, Justin W. Flatt, , Xiaodan Ma

The paper provides an overview of the EMDB archive, its current holdings, recent updates, and future plans.

Nucleic Acids Research · Oct 20, 2023Peer-reviewedBioinformatics

ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models

Brinda Kizhakke Vallat, Gerardo Tauriello, Stefan Bienert, Juergen Haas, Benjamin Webb, Augustin Žídek, Wei Hui Zheng, Ezra Peisach, Dennis W. Piehl, Ivan Anischanka, Ian Sillitoe, James L. Tolchard, Mihály Váradi, David A. Baker, Christine Anne Orengo, , John Westbrook

ModelCIF extends the PDBx/mmCIF standard to represent predicted 3D protein models, enabling FAIR data sharing for computational structural biology.

Journal of Molecular Biology · Feb 22, 2023Peer-reviewedBioinformatics

EMPIAR: The Electron Microscopy Public Image Archive

Andrii Iudin, Paul K Korir, Sriram Somasundharam, Simone N. Weyand, Cesare Cattavitello, Neli Fonseca, Osman Salih, Gerard J. Kleywegt, Ardan Patwardhan

EMPIAR provides a public archive for cryo-EM image data and 3D reconstructions, supporting data deposition, search, visualization, and programmatic access.

Nucleic Acids Research · Oct 25, 2022Peer-reviewedBioinformatics

Validation analysis of EMDB entries

Zhe Wang, Ardan Patwardhan, Gerard J. Kleywegt

The paper describes a three-tiered validation system for cryo-EM structures in EMDB, focusing on data quality and model fitting, with tier 1 providing extensive metrics and tier 3 integrating with wwPDB.

Acta Crystallographica Section D Structural Biology · Apr 20, 2022Peer-reviewedBioinformatics

The BioImage Archive - building a home for life-sciences microscopy data

Matthew Hartley, Gerard J. Kleywegt, Ardan Patwardhan, Uğis Sarkans, Jason R. Swedlow, Alvis Brāzma

The BioImage Archive provides a centralized repository for biological imaging data to enhance reproducibility, reuse, and development of image analysis tools.

Journal of Molecular Biology · Feb 18, 2022Peer-reviewedBioinformatics

3D-Strudel - a novel model-dependent map-feature validation method for high-resolution cryo-EM structures

Andrei Istrate, Zhe Wang, Garib N. Murshudov, Ardan Patwardhan, Gerard J. Kleywegt

The paper introduces 3D-Strudel, a method for validating cryo-EM maps using resolution-dependent amino-acid motifs, and presents a visualization tool for results.

bioRxiv · Dec 16, 2021 · PreprintBioinformatics