ArticleStructure (London, England : 1993)2015
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
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Article in Structure (London, England : 1993), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers.
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103citing papers in PubMed
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103 citing papers in PubMed.
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- Frontiers in integrative structural modeling of macromolecular assemblies.QRB discovery · 2025Review
- Making fluorescence-based integrative structures and associated kinetic information accessible.Nature methods · 2024Article
- The HADDOCK2.4 web server for integrative modeling of biomolecular complexes.Nature protocols · 2024Review
- Using deep-learning predictions reveals a large number of register errors in PDB depositions.IUCrJ · 2024Article
- IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.Journal of molecular biology · 2024Article
- Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.Structure (London, England : 1993) · 2024Article
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- Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins.Nature methods · 2023Article
- Coevolution and smFRET Enhances Conformation Sampling and FRET Experimental Design in Tandem PDZ1-2 Proteins.The journal of physical chemistry. B · 2023Article
- 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
- Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET.Nature communications · 2022Article
- Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines.The Journal of chemical physics · 2022Article
- New system for archiving integrative structures.Acta crystallographica. Section D, Structural biology · 2021Article
- Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.Nucleic acids research · 2021Article
- CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation.eLife · 2021Article
43 more citing papers are in PubMed but not listed here.
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Authors and funding
38 authors.
Andrej SaliDepartment of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall Room 503B, University of California, San Francisco, 1700 4(th) Street, San Francisco, CA 94158-2330, USA. Electronic address: sali@salilab.org.
Helen M BermanResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Torsten SchwedeSwiss Institute of Bioinformatics Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
Jill TrewhellaSchool of Molecular Bioscience, The University of Sydney, NSW 2006, Australia.
Gerard KleywegtProtein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Stephen K BurleyResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, 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.
John MarkleyBioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA.
Haruki NakamuraProtein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
Paul AdamsPhysical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, UC Berkeley, Berkeley, CA 94720, USA.
Alexandre M J J BonvinBijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
Wah ChiuNational Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.
Matteo Dal PeraroInstitute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
Frank Di MaioDepartment of Biochemistry, University of Washington, Seattle, WA 98195-7370, USA.
Thomas E FerrinDepartment of Pharmaceutical Chemistry and Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, 600 16(th) Street, San Francisco, CA 94158-2517, USA.
Kay GrünewaldDivision of Structural Biology, Wellcome Trust Centre of Human Genetics, University of Oxford, OX3 7BN Oxford, UK.
Aleksandras GutmanasProtein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Richard HendersonMRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Gerhard HummerDepartment of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany.
Kenji IwasakiInstitute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
Graham JohnsonDepartment of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, 600 16(th) Street, San Francisco, CA 94158-2330, USA.
Catherine L LawsonResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Jens MeilerDepartment of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA.
Marc A Marti-RenomGenome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG) and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08028 Barcelona, Spain.
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.
Michael NilgesDépartement de Biologie Structurale et Chimie, Unité de Bioinformatique Structurale, Institut Pasteur, F-75015 Paris, France; Unité Mixte de Recherche 3258, Centre National de la Recherche Scientifique, F-75015 Paris, France.
Ruth NussinovCancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
Ardan PatwardhanProtein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Juri RappsilberWellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany.
Randy J ReadDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
Helen SaibilInstitute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.
Gunnar F SchröderInstitute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany; Physics Department, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
Charles D SchwietersDivision of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-0520, USA.
Claus A M SeidelChair for Molecular Physical Chemistry, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany.
Dmitri SvergunEuropean Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.
Maya TopfInstitute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.
Eldon L UlrichBioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA.
Sameer VelankarProtein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
John D WestbrookResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Funding
VIRAL DEGENERATIVE DEMENTING DISEASE IN AGING (SUPP)P01AG002132 · NIA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 1985 to 2024
$51.7MThe Protein Structure Inittiative KnowledgebaseU01GM093324 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BERMAN, HELEN M · 2010 to 2015
$12.9MBiological Magnetic Resonance Databank: Metabolomics / Small Molecule ActivitiesP41LM005799 · NLM · UNIVERSITY OF WISCONSIN-MADISON · PI MARKLEY, JOHN LUTE · 1996 to 2013
$12.6MUnified Data Resource for Large Complexes Determined by Cryo-Electron MicroscopyR01GM079429 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2007 to 2021
$11.6MBiomedical ImagingZIACT000090 · CIT · CENTER FOR INFORMATION TECHNOLOGY · PI TRUS, BENES L · 2009 to 2018
$7.8MMedical Research Council MC_U105184322NIA NIH HHS P01 AG002132NIGMS NIH HHS GM079429NIGMS NIH HHS R01 GM079429NIGMS NIH HHS U01 GM093324NLM NIH HHS P41 LM005799NLM NIH HHS P41 LM05799Wellcome Trust 082961Wellcome Trust 088944Wellcome Trust 100140Wellcome Trust 103139Wellcome Trust 103139/Z/13/Z
Abstract
Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, on October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models?
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