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 …

Date

2025

Authors

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

Journal

Journal of Molecular Biology

Pages

169598

Publisher

Academic Press