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

Data Standard IHMCIF Integrative Modeling Open Access PDB-Dev PDBx/mmCIF Worldwide Protein Data Bank wwPDB

Journal

Journal of molecular biology
ISSN: 1089-8638
Titre abrégé: J Mol Biol
Pays: Netherlands
ID NLM: 2985088R

Informations de publication

Date de publication:
18 Mar 2024
Historique:
received: 23 01 2024
revised: 11 03 2024
accepted: 14 03 2024
medline: 21 3 2024
pubmed: 21 3 2024
entrez: 20 3 2024
Statut: aheadofprint

Résumé

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.

Identifiants

DOI: 10.1016/j.jmb.2024.168546 PMID: 38508301
pubmed: 38508301
pii: S0022-2836(24)00141-4
doi: 10.1016/j.jmb.2024.168546
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

168546

Informations de copyright

Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Auteurs

Brinda Vallat (B)

Research 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 Webb (BM)

Department 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 Westbrook (JD)

Research 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 Goddard (TD)

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.

Christian A Hanke (CA)

Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.

Andrea Graziadei (A)

Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; Human Technopole, 20157 Milan, Italy.

Ezra Peisach (E)

Research 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 Zalevsky (A)

Department 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 Sagendorf (J)

Department 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 Tangmunarunkit (H)

Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA.

Serban Voinea (S)

Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA.

Monica Sekharan (M)

Research 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 Yu (J)

Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

Alexander A M J J Bonvin (A)

Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.

Frank DiMaio (F)

Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.

Gerhard Hummer (G)

Department 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 Meiler (J)

Center 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 Tajkhorshid (E)

NIH 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 Ferrin (TE)

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.

Catherine L Lawson (CL)

Research 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 Leitner (A)

Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.

Juri Rappsilber (J)

Bioanalytics, 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 Seidel (CAM)

Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.

Cy M Jeffries (CM)

European Molecular Biology Laboratory (EMBL), Hamburg Unit, c/o Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany.

Stephen K Burley (SK)

Research 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 Hoch (JC)

Biological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, University of Connecticut, Farmington, CT 06030-3305, USA.

Genji Kurisu (G)

Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

Kyle Morris (K)

Electron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.

Ardan Patwardhan (A)

Electron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.

Sameer Velankar (S)

Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.

Torsten Schwede (T)

Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology & SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

Jill Trewhella (J)

School 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 Kesselman (C)

Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA.

Helen M Berman (HM)

Research 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 Sali (A)

Department 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.

Classifications MeSH