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

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.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [9];  [8];  [10];  [11];  [12];  [13];  [14];  [15];  [9];  [16];  [17];  [18] more »;  [19];  [20];  [21];  [22];  [23];  [11];  [12];  [24];  [25];  [26];  [27];  [9];  [28];  [29]; ORCiD logo [8];  [9];  [30];  [8] « less
  1. Rutgers Univ., Piscataway, NJ (United States); Univ. of Southern California, Los Angeles, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
  3. Utrecht Univ. (The Netherlands)
  4. The State Univ. of New Jersey, Piscataway, NJ (United States); Univ. of California, San Diego, La Jolla, CA (United States); The State Univ. of New Jersey, New Brunswick, NJ (United States)
  5. New York Structural Biology Center, New York, NY (United States); Columbia Univ., New York, NY (United States)
  6. Stanford Univ., CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)
  7. Univ. of Washington, Seattle, WA (United States)
  8. Univ. of California, San Francisco, CA (United States)
  9. The State Univ. of New Jersey, Piscataway, NJ (United States)
  10. The Scripps Research Inst., Jupiter, FL (United States)
  11. Univ. of Basel (Switzerland)
  12. Heinrich Heine Univ. Düsseldorf (Germany)
  13. UConn Health, Farmington, CT (United States)
  14. Max Planck Inst. of Biophysics, Frankfurt am Main (Germany); Goethe Univ. Frankfurt, Frankfurt am Main (Germany)
  15. Osaka Univ. (Japan)
  16. ETH Zurich (Switzerland)
  17. Univ. of Wisconsin, Madison, WI (United States)
  18. Vanderbilt Univ., Nashville, TN (United States)
  19. The State Univ. of New Jersey, Piscataway, NJ (United States); Rensselaer Polytechnic Inst., Troy, NY (United States)
  20. Rice Univ., Houston, TX (United States)
  21. Goethe Univ. Frankfurt, Frankfurt am Main (Germany)
  22. Wellcome Trust Centre for Cell Biology, Edinburgh (Scotland)
  23. Univ. of Calgary, AB (Canada)
  24. The Scripps Research Inst., La Jolla, CA (United States)
  25. European Molecular Biology Laboratory (EMBL), Hamburg (Germany)
  26. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
  27. The Univ. of Sydney (Australia); Univ. of Utah, Salt Lake City, UT (United States)
  28. European Molecular Biology Lab., European Bioinformatics Inst. (EMBL-EBI), Cambridgeshire (United Kingdom)
  29. Univ. of Leicester (United Kingdom)
  30. Univ. of Southern California, Los Angeles, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1594968
Grant/Contract Number:  
AC02-76SF00515; OAC-1838628; DBI-1756248; DBI-1756250; DBI-1519158; DBI-1832184; R01GM083960; P41GM109824
Resource Type:
Accepted Manuscript
Journal Name:
Structure
Additional Journal Information:
Journal Volume: 27; Journal Issue: 12; Journal ID: ISSN 0969-2126
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION

Citation Formats

Berman, Helen M., Adams, Paul D., Bonvin, Alexandre A., Burley, Stephen K., Carragher, Bridget, Chiu, Wah, DiMaio, Frank, Ferrin, Thomas E., Gabanyi, Margaret J., Goddard, Thomas D., Griffin, Patrick R., Haas, Juergen, Hanke, Christian A., Hoch, Jeffrey C., Hummer, Gerhard, Kurisu, Genji, Lawson, Catherine L., Leitner, Alexander, Markley, John L., Meiler, Jens, Montelione, Gaetano T., Phillips, Jr., George N., Prisner, Thomas, Rappsilber, Juri, Schriemer, David C., Schwede, Torsten, Seidel, Claus A. M., Strutzenberg, Timothy S., Svergun, Dmitri I., Tajkhorshid, Emad, Trewhella, Jill, Vallat, Brinda, Velankar, Sameer, Vuister, Geerten W., Webb, Benjamin, Westbrook, John D., White, Kate L., and Sali, Andrej. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. United States: N. p., 2019. Web. doi:10.1016/j.str.2019.11.002.
Berman, Helen M., Adams, Paul D., Bonvin, Alexandre A., Burley, Stephen K., Carragher, Bridget, Chiu, Wah, DiMaio, Frank, Ferrin, Thomas E., Gabanyi, Margaret J., Goddard, Thomas D., Griffin, Patrick R., Haas, Juergen, Hanke, Christian A., Hoch, Jeffrey C., Hummer, Gerhard, Kurisu, Genji, Lawson, Catherine L., Leitner, Alexander, Markley, John L., Meiler, Jens, Montelione, Gaetano T., Phillips, Jr., George N., Prisner, Thomas, Rappsilber, Juri, Schriemer, David C., Schwede, Torsten, Seidel, Claus A. M., Strutzenberg, Timothy S., Svergun, Dmitri I., Tajkhorshid, Emad, Trewhella, Jill, Vallat, Brinda, Velankar, Sameer, Vuister, Geerten W., Webb, Benjamin, Westbrook, John D., White, Kate L., & Sali, Andrej. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. United States. doi:10.1016/j.str.2019.11.002.
Berman, Helen M., Adams, Paul D., Bonvin, Alexandre A., Burley, Stephen K., Carragher, Bridget, Chiu, Wah, DiMaio, Frank, Ferrin, Thomas E., Gabanyi, Margaret J., Goddard, Thomas D., Griffin, Patrick R., Haas, Juergen, Hanke, Christian A., Hoch, Jeffrey C., Hummer, Gerhard, Kurisu, Genji, Lawson, Catherine L., Leitner, Alexander, Markley, John L., Meiler, Jens, Montelione, Gaetano T., Phillips, Jr., George N., Prisner, Thomas, Rappsilber, Juri, Schriemer, David C., Schwede, Torsten, Seidel, Claus A. M., Strutzenberg, Timothy S., Svergun, Dmitri I., Tajkhorshid, Emad, Trewhella, Jill, Vallat, Brinda, Velankar, Sameer, Vuister, Geerten W., Webb, Benjamin, Westbrook, John D., White, Kate L., and Sali, Andrej. Mon . "Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures". United States. doi:10.1016/j.str.2019.11.002. https://www.osti.gov/servlets/purl/1594968.
@article{osti_1594968,
title = {Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures},
author = {Berman, Helen M. and Adams, Paul D. and Bonvin, Alexandre A. and Burley, Stephen K. and Carragher, Bridget and Chiu, Wah and DiMaio, Frank and Ferrin, Thomas E. and Gabanyi, Margaret J. and Goddard, Thomas D. and Griffin, Patrick R. and Haas, Juergen and Hanke, Christian A. and Hoch, Jeffrey C. and Hummer, Gerhard and Kurisu, Genji and Lawson, Catherine L. and Leitner, Alexander and Markley, John L. and Meiler, Jens and Montelione, Gaetano T. and Phillips, Jr., George N. and Prisner, Thomas and Rappsilber, Juri and Schriemer, David C. and Schwede, Torsten and Seidel, Claus A. M. and Strutzenberg, Timothy S. and Svergun, Dmitri I. and Tajkhorshid, Emad and Trewhella, Jill and Vallat, Brinda and Velankar, Sameer and Vuister, Geerten W. and Webb, Benjamin and Westbrook, John D. and White, Kate L. and Sali, Andrej},
abstractNote = {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.},
doi = {10.1016/j.str.2019.11.002},
journal = {Structure},
number = 12,
volume = 27,
place = {United States},
year = {2019},
month = {11}
}

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