PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures.

Journal: Journal of molecular biology
Published Date: Jan 27, 2025

Abstract

Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (pdb-ihm.org), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology.

Authors

  • Brinda Vallat
    Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
  • Benjamin M Webb
    Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Quantitative Biosciences Institute (QBI), and Department of Pharmaceutical Chemistry, University of California, San Francisco., San Francisco, CA 94157, USA.
  • Arthur Zalevsky
    Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA.
  • Hongsuda Tangmunarunkit
    Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
  • Monica R Sekharan
    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.
  • Serban Voinea
    Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
  • Aref Shafaeibejestan
    Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
  • Jared Sagendorf
    Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Quantitative Biosciences Institute (QBI), and Department of Pharmaceutical Chemistry, University of California, San Francisco., San Francisco, CA 94157, USA.
  • Jeffrey C Hoch
    Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT, 06030, USA.
  • Genji Kurisu
    Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
  • Kyle L Morris
    Electron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.
  • Sameer Velankar
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
  • Carl Kesselman
    USC Information Sciences Institute, University of Southern California, Los Angeles, CA, USA.
  • Stephen K Burley
    Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, San Diego, CA, United States.
  • Helen M Berman
    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
    Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA.

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