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

Helen M Berman; Paul D Adams; Alexandre A Bonvin; Stephen K Burley; Bridget Carragher; Wah Chiu; Frank DiMaio; Thomas E Ferrin; Margaret J Gabanyi; Thomas D Goddard; Patrick R Griffin; Juergen Haas; Christian A Hanke; Jeffrey C Hoch; Gerhard Hummer; Genji Kurisu; Catherine L Lawson; Alexander Leitner; John L Markley; Jens Meiler; Gaetano T Montelione; George N Phillips Jr; Thomas Prisner; Juri Rappsilber; David C Schriemer; Torsten Schwede; Claus A M Seidel; Timothy S Strutzenberg; Dmitri I Svergun; Emad Tajkhorshid; Jill Trewhella; Brinda Vallat; Sameer Velankar; Geerten W Vuister; Benjamin Webb; John D Westbrook; Kate L White; Andrej Sali

doi:10.1016/j.str.2019.11.002

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

Structure. 2019 Dec 3;27(12):1745-1759. doi: 10.1016/j.str.2019.11.002. Epub 2019 Nov 25.

Authors

Helen M Berman¹, Paul D Adams², Alexandre A Bonvin³, Stephen K Burley⁴, Bridget Carragher⁵, Wah Chiu⁶, Frank DiMaio⁷, Thomas E Ferrin⁸, Margaret J Gabanyi⁹, Thomas D Goddard⁸, Patrick R Griffin¹⁰, Juergen Haas¹¹, Christian A Hanke¹², Jeffrey C Hoch¹³, Gerhard Hummer¹⁴, Genji Kurisu¹⁵, Catherine L Lawson⁹, Alexander Leitner¹⁶, John L Markley¹⁷, Jens Meiler¹⁸, Gaetano T Montelione¹⁹, George N Phillips Jr²⁰, Thomas Prisner²¹, Juri Rappsilber²², David C Schriemer²³, Torsten Schwede¹¹, Claus A M Seidel¹², Timothy S Strutzenberg¹⁰, Dmitri I Svergun²⁴, Emad Tajkhorshid²⁵, Jill Trewhella²⁶, Brinda Vallat⁹, Sameer Velankar²⁷, Geerten W Vuister²⁸, Benjamin Webb²⁹, John D Westbrook³⁰, Kate L White³¹, Andrej Sali³²

Affiliations

¹ 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.
² Physical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, University of California-Berkeley, Berkeley, CA 94720, USA.
³ Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
⁴ 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.
⁵ 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.
⁶ Department of Bioengineering, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305-5447, USA; SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
⁷ Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
⁸ Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
⁹ Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
¹⁰ The Scripps Research Institute, Jupiter, FL 33458, USA.
¹¹ Swiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland.
¹² Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
¹³ Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA.
¹⁴ 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.
¹⁵ Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
¹⁶ Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
¹⁷ BioMagResBank (BMRB), Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
¹⁸ Center for Structural Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37221, USA.
¹⁹ 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.
²⁰ BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX 77251, USA.
²¹ Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
²² Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3JR, Scotland.
²³ Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, Calgary, AB T2N 4N1, Canada.
²⁴ European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany.
²⁵ 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.
²⁶ 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.
²⁷ Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK.
²⁸ Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK.
²⁹ Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
³⁰ 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.
³¹ 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.
³² 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.

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.

Publication types

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

MeSH terms

Computational Biology / methods*
Crystallography, X-Ray
Databases, Protein*
Magnetic Resonance Spectroscopy
Models, Molecular*
Protein Conformation*
Proteins / chemistry*

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding