ArticleStructure (London, England : 1993)2019
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
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Article in Structure (London, England : 1993), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26citing papers in PubMed
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Who cites it
26 citing papers in PubMed.
- IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank.Journal of molecular biology · 2026Article
- The NMR Exchange Format (NEF): Specification and Applications.bioRxiv : the preprint server for biology · 2026Article
- RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models.Nucleic acids research · 2026Article
- PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures.Journal of molecular biology · 2025Article
- ModelArchive: A Deposition Database for Computational Macromolecular Structural Models.Journal of molecular biology · 2025Article
- tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling.Bioinformatics (Oxford, England) · 2025Article
- Making fluorescence-based integrative structures and associated kinetic information accessible.Nature methods · 2024Article
- IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.Journal of molecular biology · 2024Article
- Article
- Article
- Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins.Nature methods · 2023Article
- RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
- Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.Biophysical reviews · 2022Review
- Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.Biomolecules · 2022Review
- Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy.Annual review of biochemistry · 2022Review
- Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules.Journal of the American Chemical Society · 2021Article
- Bayesian metamodeling of complex biological systems across varying representations.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction.Structure (London, England : 1993) · 2021Review
- FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.eLife · 2021Review
- The Protein Data Bank Archive.Methods in molecular biology (Clifton, N.J.) · 2021Review
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Authors and funding
38 authors.
Helen M BermanDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA. Electronic address: hb_093@usc.edu.
Paul D AdamsPhysical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, University of California-Berkeley, Berkeley, CA 94720, USA.
Alexandre A BonvinBijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
Stephen K BurleyResearch Collaboratory for Structural Bioinformatics Protein Data Bank, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA.
Bridget CarragherSimons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Wah ChiuDepartment of Bioengineering, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305-5447, USA; SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Frank DiMaioDepartment of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Thomas E FerrinDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
Margaret J GabanyiInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Thomas D GoddardDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
Patrick R GriffinThe Scripps Research Institute, Jupiter, FL 33458, USA.
Juergen HaasSwiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland.
Christian A HankeMolecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
Jeffrey C HochDepartment of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, 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.
Genji KurisuProtein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
Catherine L LawsonInstitute 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.
John L MarkleyBioMagResBank (BMRB), Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
Jens MeilerCenter for Structural Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37221, USA.
Gaetano T MontelioneCenter for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytech Institute, Troy, NY 12180, USA.
George N PhillipsBioSciences at Rice and Department of Chemistry, Rice University, Houston, TX 77251, USA.
Thomas PrisnerInstitute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
Juri RappsilberWellcome Trust Centre for Cell Biology, Edinburgh EH9 3JR, Scotland.
David C SchriemerDepartment of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, Calgary, AB T2N 4N1, Canada.
Torsten SchwedeSwiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland.
Claus A M SeidelMolecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
Timothy S StrutzenbergThe Scripps Research Institute, Jupiter, FL 33458, USA.
Dmitri I SvergunEuropean Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany.
Emad TajkhorshidDepartment of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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.
Brinda VallatInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Sameer VelankarProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK.
Geerten W VuisterDepartment of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK.
Benjamin WebbDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
John D WestbrookResearch Collaboratory for Structural Bioinformatics Protein Data Bank, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Kate L WhiteDepartment of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA.
Andrej SaliDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: sali@salilab.org.
Funding
PROJECT 5 - DUKE - STRUCTURE VALIDATION AND IMPROVEMENT FOR PROTEINS AND N. ACIDSP01GM063210 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI ADAMS, PAUL DAVID · 2001 to 2021
$33.5MPDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICSR01GM133198 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BURLEY, STEPHEN K · 2019 to 2023
$19.3MTR&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
$18.8MIMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2MProtein structure determination from low-resolution experimental dataR01GM123089 · NIGMS · UNIVERSITY OF WASHINGTON · PI DIMAIO, FRANK P · 2017 to 2025
$2.6MMedical Research Council MR/L000555/1Medical Research Council MR/P00038X/1NIGMS NIH HHS P01 GM063210NIGMS NIH HHS P41 GM109824NIGMS NIH HHS R01 GM083960NIGMS NIH HHS R01 GM123089NIGMS NIH HHS R01 GM133198Wellcome Trust 103139/Z/13/Z
Abstract
Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here.
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Databases, ProteinModels, MolecularProtein ConformationComputational BiologyCrystallography, X-RayMagnetic Resonance SpectroscopyProteinsProteins
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