Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

Andrej Sali; Helen M Berman; Torsten Schwede; Jill Trewhella; Gerard Kleywegt; Stephen K Burley; John Markley; Haruki Nakamura; Paul Adams; Alexandre M J J Bonvin; Wah Chiu; Matteo Dal Peraro; Frank Di Maio; Thomas E Ferrin; Kay Grünewald; Aleksandras Gutmanas; Richard Henderson; Gerhard Hummer; Kenji Iwasaki; Graham Johnson; Catherine L Lawson; Jens Meiler; Marc A Marti-Renom; Gaetano T Montelione; Michael Nilges; Ruth Nussinov; Ardan Patwardhan; Juri Rappsilber; Randy J Read; Helen Saibil; Gunnar F Schröder; Charles D Schwieters; Claus A M Seidel; Dmitri Svergun; Maya Topf; Eldon L Ulrich; Sameer Velankar; John D Westbrook

doi:10.1016/j.str.2015.05.013

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

Structure. 2015 Jul 7;23(7):1156-67. doi: 10.1016/j.str.2015.05.013. Epub 2015 Jun 18.

Authors

Andrej Sali¹, Helen M Berman², Torsten Schwede³, Jill Trewhella⁴, Gerard Kleywegt⁵, Stephen K Burley⁶, John Markley⁷, Haruki Nakamura⁸, Paul Adams⁹, Alexandre M J J Bonvin¹⁰, Wah Chiu¹¹, Matteo Dal Peraro¹², Frank Di Maio¹³, Thomas E Ferrin¹⁴, Kay Grünewald¹⁵, Aleksandras Gutmanas⁵, Richard Henderson¹⁶, Gerhard Hummer¹⁷, Kenji Iwasaki¹⁸, Graham Johnson¹⁹, Catherine L Lawson², Jens Meiler²⁰, Marc A Marti-Renom²¹, Gaetano T Montelione²², Michael Nilges²³, Ruth Nussinov²⁴, Ardan Patwardhan⁵, Juri Rappsilber²⁵, Randy J Read²⁶, Helen Saibil²⁷, Gunnar F Schröder²⁸, Charles D Schwieters²⁹, Claus A M Seidel³⁰, Dmitri Svergun³¹, Maya Topf²⁷, Eldon L Ulrich⁷, Sameer Velankar⁵, John D Westbrook²

Affiliations

¹ Department 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.
² Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
³ Swiss Institute of Bioinformatics Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
⁴ School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia.
⁵ Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
⁶ Research 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.
⁷ BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA.
⁸ Protein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
⁹ Physical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, UC Berkeley, Berkeley, CA 94720, USA.
¹⁰ Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
¹¹ National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.
¹² Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
¹³ Department of Biochemistry, University of Washington, Seattle, WA 98195-7370, USA.
¹⁴ Department 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.
¹⁵ Division of Structural Biology, Wellcome Trust Centre of Human Genetics, University of Oxford, OX3 7BN Oxford, UK.
¹⁶ MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
¹⁷ Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany.
¹⁸ Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
¹⁹ Department 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.
²⁰ Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA.
²¹ Genome 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.
²² Center 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.
²³ Département 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.
²⁴ Cancer 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.
²⁵ Wellcome 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.
²⁶ Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
²⁷ Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.
²⁸ Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany; Physics Department, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
²⁹ Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-0520, USA.
³⁰ Chair for Molecular Physical Chemistry, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany.
³¹ European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.

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?

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Advisory Committees
Computational Biology
Databases, Protein*
Humans
Models, Molecular
Protein Conformation
Proteins / chemistry*

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding