IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods

• DOI: 10.1016/j.jmb.2024.168546
• Publication Date: 2024-03-18T16:20:36Z
• Authors: Brinda Vallat; Benjamin M. Webb; John D. Westbrook; Thomas D. Goddard; Christian A. Hanke; Andrea Graziadei; Ezra Peisach; Arthur Zalevsky; Jared Sagendorf; Hongsuda Tangmuna...; Serban Voinea; Monica Sekharan; Jian Yu; Alexander A.M.J.J...; Frank DiMaio; Gerhard Hummer; Jens Meiler; Emad Tajkhorshid; Thomas E. Ferrin; Catherine L. Lawson; Alexander Leitner; Juri Rappsilber; Claus A.M. Seidel; Cy M. Jeffries; Stephen K. Burley; Jeffrey C. Hoch; Genji Kurisu; Kyle Morris; Ardan Patwardhan; Sameer Velankar; Torsten Schwede; Jill Trewhella; Carl Kesselman; Helen M. Berman; Andrej Sali
• Keywords: 570; Crystallography; Protein Conformation; Macromolecular Substances; Protein; PDB-Dev; Proteins; Molecular; Computational Biology; Ligands; Databases; Models; X-Ray; IHMCIF; PDBx/mmCIF; ddc:570; Data Standard; Software; Worldwide Protein Data Bank

IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB.