Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.,Structure

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Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
Structure ( IF 4.4 ) Pub Date : 2019-11-25 , DOI: 10.1016/j.str.2019.11.002
Helen M Berman ₁ , Paul D Adams ₂ , Alexandre A Bonvin ₃ , Stephen K Burley ₄ , Bridget Carragher ₅ , Wah Chiu ₆ , Frank DiMaio ₇ , Thomas E Ferrin ₈ , Margaret J Gabanyi ₉ , Thomas D Goddard ₈ , Patrick R Griffin ₁₀ , Juergen Haas ₁₁ , Christian A Hanke ₁₂ , Jeffrey C Hoch ₁₃ , Gerhard Hummer ₁₄ , Genji Kurisu ₁₅ , Catherine L Lawson ₉ , Alexander Leitner ₁₆ , John L Markley ₁₇ , Jens Meiler ₁₈ , Gaetano T Montelione ₁₉ , George N Phillips ₂₀ , Thomas Prisner ₂₁ , Juri Rappsilber ₂₂ , David C Schriemer ₂₃ , Torsten Schwede ₁₁ , Claus A M Seidel ₁₂ , Timothy S Strutzenberg ₁₀ , Dmitri I Svergun ₂₄ , Emad Tajkhorshid ₂₅ , Jill Trewhella ₂₆ , Brinda Vallat ₉ , Sameer Velankar ₂₇ , Geerten W Vuister ₂₈ , Benjamin Webb ₂₉ , John D Westbrook ₃₀ , Kate L White ₃₁ , Andrej Sali ₃₂

Affiliation

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.
Physical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, University of California-Berkeley, Berkeley, CA 94720, USA.
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
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.
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.
Department of Bioengineering, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305-5447, USA; SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
The Scripps Research Institute, Jupiter, FL 33458, USA.
Swiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland.
Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA.
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.
Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
BioMagResBank (BMRB), Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
Center for Structural Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37221, USA.
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.
BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX 77251, USA.
Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3JR, Scotland.
Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, Calgary, AB T2N 4N1, Canada.
European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany.
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.
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.
Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK.
Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK.
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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.
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.
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.

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.

中文翻译：

联合结构模型和数据：归档集成结构研讨会的成果。

生物分子系统的结构越来越多地通过综合建模来计算。在这种方法中，结构模型是通过组合来自多个来源的信息来构建的，包括各种实验方法和先前的模型。2019 年，作为生物物理学会卫星会议举办了一次研讨会，以评估进展并讨论归档综合结构的进一步要求。研讨会的主要目标是就解决创建通用数据标准、构建联合数据交换方法以及开发验证集成结构的机制所涉及的挑战达成共识。研讨会摘要和提出的建议在此处介绍。

更新日期：2019-11-26

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