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Vallat B, Webb BM, Zalevsky A, Tangmunarunkit H, Sekharan MR, Voinea S, Shafaeibejestan A, Sagendorf J, Hoch JC, Kurisu G, Morris KL, Velankar S, Kesselman C, Burley SK, Berman HM, Sali A. PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures. J Mol Biol 2025:168963. [PMID: 40110969 DOI: 10.1016/j.jmb.2025.168963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Revised: 01/21/2025] [Accepted: 01/22/2025] [Indexed: 03/22/2025]
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.
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Affiliation(s)
- Brinda Vallat
- 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; Rutgers Cancer Institute, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, 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, Quantitative Biosciences Institute (QBI), and Department of Pharmaceutical Chemistry, University of California, San Francisco., San Francisco, CA 94157, 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
- Biological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, University of Connecticut, Farmington, CT 06030-3305, 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
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Carl Kesselman
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Stephen K Burley
- 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; Rutgers Cancer Institute, 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; Rutgers Artificial Intelligence and Data Science (RAD) Collaboratory, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - 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, Quantitative Biosciences Institute (QBI), and Department of Pharmaceutical Chemistry, University of California, San Francisco., San Francisco, CA 94157, USA
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Hennig J, Paulino C. 4D structural biology-The 9 th Murnau Conference on structural biology. Structure 2025; 33:1-5. [PMID: 39753099 DOI: 10.1016/j.str.2024.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 11/13/2024] [Accepted: 11/18/2024] [Indexed: 01/11/2025]
Abstract
The data presented at the 9th International Murnau Conference on September 18-21, 2024, the largest recurring structural biology meeting in Central Europe, illustrated the thriving state of the structural biology community. This is largely attributed to the ground-breaking developments over the last decade, which were intensely discussed during the meeting.
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Affiliation(s)
- Janosch Hennig
- Chair Biochemistry IV, Biophysical Chemistry, University of Bayreuth, 95448 Bayreuth, Germany; Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117 Heidelberg, Germany.
| | - Cristina Paulino
- Biochemistry Center Heidelberg, Heidelberg University, 69120 Heidelberg, Germany.
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Hanke CA, Westbrook JD, Webb BM, Peulen TO, Lawson CL, Sali A, Berman HM, Seidel CAM, Vallat B. Making fluorescence-based integrative structures and associated kinetic information accessible. Nat Methods 2024; 21:1970-1972. [PMID: 39349602 PMCID: PMC11939118 DOI: 10.1038/s41592-024-02428-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2024]
Affiliation(s)
- Christian A Hanke
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Benjamin M Webb
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, California, USA
| | - Thomas-O Peulen
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, California, USA
- Physical Chemistry, TU Dortmund University, Dortmund, Germany
| | - Catherine L Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, California, USA
| | - 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, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
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