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

PDB-IHM is a branch of the Protein Data Bank (PDB), a Worldwide Protein Data Bank (wwPDB) Core Archive, that expands its scope by allowing for additional biomolecular structure representations and types of experimental information (i.e., integrative/hybrid structure models). As of October 2025, PDB-IHM contained 374 entries, benefitting from multi-scale and multi-state representations and 17 types of experimental data. These structure models are assigned PDB accession codes and are archived alongside other experimental structures in the PDB. Rigorous interpretation of a structure model requires assessment of underlying data quality, consistency with the input data, and estimates of positional uncertainty of its components. Herein, we present the IHMValidation pipeline (https://validate.pdb-ihm.org; https://github.com/salilab/IHMValidation) based on recommendations from the wwPDB Integrative Methods Task Force plus the small-angle scattering (SAS), chemical crosslinking mass spectrometry (crosslinking-MS), and cryo-electron microscopy and tomography (3DEM) communities. The IHMValidation report (available in both PDF and HTML formats) comprises six sections: (i) overview; (ii) model details; (iii) data quality assessments; (iv) local geometry assessments (i.e., model quality); (v) fit of the model to the data used to generate it; and (vi) fit of the model to the data used for validation. Future expansions of the IHMValidation pipeline will: (i) reflect recommendations coming from additional experimental communities, including Förster resonance energy transfer (FRET) and hydrogen/deuterium exchange MS (HDX-MS); (ii) include other validation criteria, such as Bayesian likelihoods for the data; and (iii) represent estimates of structure model uncertainty based on the variation among alternative models satisfying input data.

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Journal
Journal of Molecular Biology
Published
2025-12-01
DOI
https://doi.org/10.1016/j.jmb.2025.169598
Primary Topic
Enzyme Structure and Function
Type
article
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article

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

Alexander Leitner, Ezra Peisach, Jasmine Y. Young, Hongsuda Tangmunarunkit et al.
Journal of Molecular Biology
Enzyme Structure and Function
article

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

Alexander Leitner, Ezra Peisach, Jasmine Y. Young, Hongsuda Tangmunarunkit, Arthur O. Zalevsky, Benjamin Webb, Justin W. Flatt, Andrea Graziadei, Kyle L. Morris, Genji Kurisu, Jill Trewhella, Andrej Săli, Jared Sagendorf, Brinda Vallat, Sameer S Velankar, Juan Antonio Vizcaíno, Jeffrey C. Hoch, Shruthi Viswanath, S.K. Burley, Helen M. Berman, Monica R. Sekharan, Juri Rappsilber, Sai J. Ganesan, Carl Kesselman, Aref Shafaeibejestan, Kartik Majila, Cy M. Jeffries
article en

Abstract

PDB-IHM is a branch of the Protein Data Bank (PDB), a Worldwide Protein Data Bank (wwPDB) Core Archive, that expands its scope by allowing for additional biomolecular structure representations and types of experimental information (i.e., integrative/hybrid structure models). As of October 2025, PDB-IHM contained 374 entries, benefitting from multi-scale and multi-state representations and 17 types of experimental data. These structure models are assigned PDB accession codes and are archived alongside other experimental structures in the PDB. Rigorous interpretation of a structure model requires assessment of underlying data quality, consistency with the input data, and estimates of positional uncertainty of its components. Herein, we present the IHMValidation pipeline (https://validate.pdb-ihm.org; https://github.com/salilab/IHMValidation) based on recommendations from the wwPDB Integrative Methods Task Force plus the small-angle scattering (SAS), chemical crosslinking mass spectrometry (crosslinking-MS), and cryo-electron microscopy and tomography (3DEM) communities. The IHMValidation report (available in both PDF and HTML formats) comprises six sections: (i) overview; (ii) model details; (iii) data quality assessments; (iv) local geometry assessments (i.e., model quality); (v) fit of the model to the data used to generate it; and (vi) fit of the model to the data used for validation. Future expansions of the IHMValidation pipeline will: (i) reflect recommendations coming from additional experimental communities, including Förster resonance energy transfer (FRET) and hydrogen/deuterium exchange MS (HDX-MS); (ii) include other validation criteria, such as Bayesian likelihoods for the data; and (iii) represent estimates of structure model uncertainty based on the variation among alternative models satisfying input data.

Journal of Molecular Biology
Rutgers, The State University of New Jersey (US), QB3 (US), University of Southern California (US), European Bioinformatics Institute (GB), National Centre for Biological Sciences (IN), University of Utah (US), Deutsches Elektronen-Synchrotron DESY (DE), ETH Zurich (CH), Human Technopole (IT), Protein Research Foundation (JP), Resonance Research (United States) (US), Technische Universität Berlin (DE), The University of Osaka (JP)
Openalex Percentile: Top 66%
Enzyme Structure and Function
DOIOpen Access PDFOpenAlex
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