
@article {162693,
	title = {IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank.},
	journal = {J Mol Biol},
	year = {2025},
	month = {2025 Dec 18},
	pages = {169598},
	abstract = {<p>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 F{\"o}rster 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.</p>
},
	issn = {1089-8638},
	doi = {10.1016/j.jmb.2025.169598},
	author = {Zalevsky, Arthur O and Vallat, Brinda and Webb, Benjamin M and Tangmunarunkit, Hongsuda and Sekharan, Monica R and Shafaeibejestan, Aref and Ganesan, Sai and Sagendorf, Jared and Jeffries, Cy M and Trewhella, Jill and Graziadei, Andrea and Vizca{\'\i}no, Juan Antonio and Leitner, Alexander and Rappsilber, Juri and Peisach, Ezra and Flatt, Justin W and Young, Jasmine Y and Majila, Kartik and Viswanath, Shruthi and Kesselman, Carl and Hoch, Jeffrey C and Kurisu, Genji and Morris, Kyle L and Velankar, Sameer and Berman, Helen M and Burley, Stephen K and Sali, Andrej}
}
