Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
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Berman HM
Department 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.
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Adams PD
Physical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, University of California-Berkeley, Berkeley, CA 94720, USA.
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Bonvin AA
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
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Burley SK
Research 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.
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Carragher B
Simons 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.
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Chiu W
Department of Bioengineering, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305-5447, USA; SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
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DiMaio F
Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
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Ferrin TE
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
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Gabanyi MJ
Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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Goddard TD
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
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Griffin PR
The Scripps Research Institute, Jupiter, FL 33458, USA.
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Haas J
Swiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland.
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Hanke CA
Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
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Hoch JC
Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA.
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Hummer G
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
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Kurisu G
Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
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Lawson CL
Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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Leitner A
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
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Markley JL
BioMagResBank (BMRB), Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Meiler J
Center for Structural Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37221, USA.
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Montelione GT
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; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytech Institute, Troy, NY 12180, USA.
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Phillips GN
BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX 77251, USA.
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Prisner T
Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
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Rappsilber J
Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3JR, Scotland.
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Schriemer DC
Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, Calgary, AB T2N 4N1, Canada.
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Schwede T
Swiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland.
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Seidel CAM
Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
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Strutzenberg TS
The Scripps Research Institute, Jupiter, FL 33458, USA.
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Svergun DI
European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany.
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Tajkhorshid E
Department 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.
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Trewhella J
School 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.
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Vallat B
Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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Velankar S
Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK.
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Vuister GW
Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK.
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Webb B
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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Westbrook JD
Research 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.
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White KL
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.
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Sali A
Department 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.
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Published in:
- Structure (London, England : 1993). - 2019
English
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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bronze
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https://sonar.ch/global/documents/186156
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