ArticleJournal of molecular biology2024
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.
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Article in Journal of molecular biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8citing papers in PubMed
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8 citing papers in PubMed.
- IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank.Journal of molecular biology · 2026Article
- ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models.Journal of molecular biology · 2026Article
- RCSB protein data Bank: Next-generation advanced search for exploration of experimental structures and computed structure models.Protein science : a publication of the Protein Society · 2026Article
- Protein Data Bank (PDB) Archive: a new architecture (beta) for scalable, PDBx/mmCIF-based data distribution.Acta crystallographica. Section D, Structural biology · 2026Article
- RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models.Nucleic acids research · 2026Article
- Ten rules for a structural bioinformatic analysis.PLoS computational biology · 2025Article
- PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures.Journal of molecular biology · 2025Article
- Making fluorescence-based integrative structures and associated kinetic information accessible.Nature methods · 2024Article
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Authors and funding
35 authors.
Brinda VallatResearch Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA. Electronic address: brinda.vallat@rcsb.org.
Benjamin M WebbDepartment of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, the Quantitative Biosciences Institute (QBI), and the Research Collaboratory for Structural Bioinformatics Protein Data Bank, University of California, San Francisco, San Francisco, CA 94157, USA.
John D WestbrookResearch Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
Thomas D GoddardDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
Christian A HankeMolecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
Andrea GraziadeiBioanalytics, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; Human Technopole, 20157 Milan, Italy.
Ezra PeisachResearch Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Arthur ZalevskyDepartment of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, the Quantitative Biosciences Institute (QBI), and the Research Collaboratory for Structural Bioinformatics Protein Data Bank, University of California, San Francisco, San Francisco, CA 94157, USA.
Jared SagendorfDepartment of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, the Quantitative Biosciences Institute (QBI), and the Research Collaboratory for Structural Bioinformatics Protein Data Bank, University of California, San Francisco, San Francisco, CA 94157, USA.
Hongsuda TangmunarunkitInformation Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
Serban VoineaInformation Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
Monica SekharanResearch Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Jian YuProtein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
Alexander A M J J BonvinBijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
Frank DiMaioDepartment of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Gerhard HummerDepartment of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
Jens MeilerCenter for Structural Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37221, USA; Institute for Drug Discovery, Leipzig University Medical School, 04103 Leipzig, Germany.
Emad TajkhorshidNIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Thomas E FerrinDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
Catherine L LawsonResearch Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Alexander LeitnerDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
Juri RappsilberBioanalytics, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK.
Claus A M SeidelMolecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
Cy M JeffriesEuropean Molecular Biology Laboratory (EMBL), Hamburg Unit, c/o Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany.
Stephen K BurleyResearch Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Jeffrey C HochBiological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, University of Connecticut, Farmington, CT 06030-3305, USA.
Genji KurisuProtein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
Kyle MorrisElectron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
Ardan PatwardhanElectron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
Sameer VelankarProtein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.
Torsten SchwedeBiozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology & SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
Jill TrewhellaSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
Carl KesselmanInformation Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
Helen M BermanResearch Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles CA 90089, USA.
Andrej SaliDepartment of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, the Quantitative Biosciences Institute (QBI), and the Research Collaboratory for Structural Bioinformatics Protein Data Bank, University of California, San Francisco, San Francisco, CA 94157, USA.
Funding
PDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICSR01GM133198 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BURLEY, STEPHEN K · 2019 to 2023
$19.3MWHOLE CELL SIMULATIONP41GM104601 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI TAJKHORSHID, EMAD · 2012 to 2021
$19.0MTR&D Project 4. The Imaging Stage: Multiscale Spatiotemporal Modeling of Macromolecular Systems in Cellular NeighborhoodsP41GM109824 · NIGMS · ROCKEFELLER UNIVERSITY · PI ROUT, MICHAEL P · 2014 to 2023
$18.8MDecrypting Variants of Uncertain Significance in Long-QT SyndromeR01HL122010 · NHLBI · VANDERBILT UNIVERSITY · PI GEORGE, ALFRED L., SANDERS, CHARLES R · 2014 to 2025
$15.5MPDB Management by the Research Collaboratory for Structural BioinformaticsR01GM157729 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI STEPHEN K BURLEY · 2024 to 2026
$11.6MResource for Macromolecular Modeling and VisualizationR24GM145965 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI Emad Tajkhorshid · 2022 to 2026
$6.2MStructure based design of trimer interface epitope focused universal influenza vaccinesU01AI150739 · NIAID · VANDERBILT UNIVERSITY MEDICAL CENTER · PI CROWE, JAMES E · 2020 to 2024
$6.1MChimeraX -- Next Generation Visualization and Analysis Software for Multiscale ModelingR01GM129325 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERRIN, THOMAS E · 2018 to 2025
$5.2MIMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2MBiological Magnetic Resonance Data BankR24GM150793 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI JEFFREY C HOCH · 2023 to 2026
$3.0MStructural Determinants of Allosteric Modulation of Brain GPCRsR01DA046138 · NIDA · VANDERBILT UNIVERSITY · PI MEILER, JENS · 2019 to 2023
$2.0MMechanistic insights into Variants of Uncertain Significance (VUS) using novel EGFR variants as a paradigmR01CA227833 · NCI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI LOVLY, CHRISTINE M., MEILER, JENS · 2019 to 2023
$1.7MNCI NIH HHS R01 CA227833NHLBI NIH HHS R01 HL122010NIAID NIH HHS U01 AI150739NIDA NIH HHS R01 DA046138NIGMS NIH HHS P41 GM104601NIGMS NIH HHS P41 GM109824NIGMS NIH HHS R01 GM083960NIGMS NIH HHS R01 GM129325NIGMS NIH HHS R01 GM133198NIGMS NIH HHS R01 GM157729NIGMS NIH HHS R24 GM145965NIGMS NIH HHS R24 GM150793NIH HHS S10 OD016216NIH HHS S10 OD020154NIH HHS S10 OD032234Wellcome Trust
Abstract
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.
Indexed as
Databases, ProteinProteinsComputational BiologyCrystallography, X-RayLigandsMacromolecular SubstancesModels, MolecularProtein ConformationSoftwareLigandsMacromolecular SubstancesProteinsData StandardIHMCIFPDB-DevPDBx/mmCIFWorldwide Protein Data Bank
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