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Title: An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Abstract

Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [5];  [9];  [7];  [8];  [10];  [11];  [9]; ORCiD logo [9];  [11];  [11];  [12]; ORCiD logo [13] more »;  [5];  [14];  [14];  [15];  [16];  [17];  [11];  [13];  [18];  [5];  [11];  [11];  [2];  [19];  [20];  [11];  [16];  [17];  [14]; ORCiD logo [16];  [1];  [11];  [11]; ORCiD logo [11];  [15];  [16];  [14];  [11];  [21];  [22];  [23];  [23];  [17];  [24];  [8];  [17];  [17];  [17];  [11];  [17];  [5];  [11]; ORCiD logo [8];  [16];  [11]; ORCiD logo [23];  [25];  [21];  [13]; ORCiD logo [19];  [9]; ORCiD logo [5];  [26] « less
+ Show Author Affiliations
  1. Ben Gurion Univ. of the Negev, Be'er sheva (Israel)
  2. Univ. of Reading (United Kingdom)
  3. Linköping Univ. (Sweden)
  4. Purdue Univ., West Lafayette, IN (United States)
  5. Univ. of Missouri, Columbia, MO (United States)
  6. Univ. of Missouri, Columbia, MO (United States); Auburn Univ., AL (United States)
  7. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  8. Univ. of Sao Paulo (Brazil)
  9. Indian Inst. of Science, Bangalore (India)
  10. Research and Information Systems, LLC, Carmel, IN (United States);; IU School of Medicine, Indianapolis, IN (United States); The Research Inst. at Nationwide Children's Hospital, Columbus, OH (United States)
  11. Univ. of Gdansk (Poland)
  12. Univ. of California, Merced, CA (United States)
  13. Seoul National Univ. (Korea, Republic of)
  14. Univ. of Massachusetts, Dartmouth, MA (United States)
  15. Princeton Univ., NJ (United States)
  16. Texas A & M Univ., College Station, TX (United States)
  17. Univ. of Washington, Seattle, WA (United States)
  18. Univ. of Missouri, Columbia, MO (United States); NorthEast Normal Univ., Changchun (China)
  19. Max Planck Inst. for Biophysical Chemistry, Gottingen (Germany)
  20. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); California Polytechnic State Univ. (CalPoly), Paloma, CA (United States)
  21. Cornell Univ., Ithaca, NY (United States)
  22. Univ. of Michigan, Ann Arbor, MI (United States)
  23. Univ. of Gdansk (Poland); Medical Univ. of Gdansk (Poland)
  24. Northeastern Univ., Boston, MA (United States)
  25. Stanford Univ., CA (United States)
  26. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Davis, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
Contributing Org.:
Foldit Players consortium
OSTI Identifier:
1478361
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Keasar, Chen, McGuffin, Liam J., Wallner, Björn, Chopra, Gaurav, Adhikari, Badri, Bhattacharya, Debswapna, Blake, Lauren, Bortot, Leandro Oliveira, Cao, Renzhi, Dhanasekaran, B. K., Dimas, Itzhel, Faccioli, Rodrigo Antonio, Faraggi, Eshel, Ganzynkowicz, Robert, Ghosh, Sambit, Ghosh, Soma, Giełdoń, Artur, Golon, Lukasz, He, Yi, Heo, Lim, Hou, Jie, Khan, Main, Khatib, Firas, Khoury, George A., Kieslich, Chris, Kim, David E., Krupa, Pawel, Lee, Gyu Rie, Li, Hongbo, Li, Jilong, Lipska, Agnieszka, Liwo, Adam, Maghrabi, Ali Hassan A., Mirdita, Milot, Mirzaei, Shokoufeh, Mozolewska, Magdalena A., Onel, Melis, Ovchinnikov, Sergey, Shah, Anand, Shah, Utkarsh, Sidi, Tomer, Sieradzan, Adam K., Ślusarz, Magdalena, Ślusarz, Rafal, Smadbeck, James, Tamamis, Phanourios, Trieber, Nicholas, Wirecki, Tomasz, Yin, Yanping, Zhang, Yang, Bacardit, Jaume, Baranowski, Maciej, Chapman, Nicholas, Cooper, Seth, Defelicibus, Alexandre, Flatten, Jeff, Koepnick, Brian, Popović, Zoran, Zaborowski, Bartlomiej, Baker, David, Cheng, Jianlin, Czaplewski, Cezary, Delbem, Alexandre Cláudio Botazzo, Floudas, Christodoulos, Kloczkowski, Andrzej, Ołdziej, Stanislaw, Levitt, Michael, Scheraga, Harold, Seok, Chaok, Söding, Johannes, Vishveshwara, Saraswathi, Xu, Dong, and Crivelli, Silvia N. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. United States: N. p., 2018. Web. doi:10.1038/s41598-018-26812-8.
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Keasar, Chen, McGuffin, Liam J., Wallner, Björn, Chopra, Gaurav, Adhikari, Badri, Bhattacharya, Debswapna, Blake, Lauren, Bortot, Leandro Oliveira, Cao, Renzhi, Dhanasekaran, B. K., Dimas, Itzhel, Faccioli, Rodrigo Antonio, Faraggi, Eshel, Ganzynkowicz, Robert, Ghosh, Sambit, Ghosh, Soma, Giełdoń, Artur, Golon, Lukasz, He, Yi, Heo, Lim, Hou, Jie, Khan, Main, Khatib, Firas, Khoury, George A., Kieslich, Chris, Kim, David E., Krupa, Pawel, Lee, Gyu Rie, Li, Hongbo, Li, Jilong, Lipska, Agnieszka, Liwo, Adam, Maghrabi, Ali Hassan A., Mirdita, Milot, Mirzaei, Shokoufeh, Mozolewska, Magdalena A., Onel, Melis, Ovchinnikov, Sergey, Shah, Anand, Shah, Utkarsh, Sidi, Tomer, Sieradzan, Adam K., Ślusarz, Magdalena, Ślusarz, Rafal, Smadbeck, James, Tamamis, Phanourios, Trieber, Nicholas, Wirecki, Tomasz, Yin, Yanping, Zhang, Yang, Bacardit, Jaume, Baranowski, Maciej, Chapman, Nicholas, Cooper, Seth, Defelicibus, Alexandre, Flatten, Jeff, Koepnick, Brian, Popović, Zoran, Zaborowski, Bartlomiej, Baker, David, Cheng, Jianlin, Czaplewski, Cezary, Delbem, Alexandre Cláudio Botazzo, Floudas, Christodoulos, Kloczkowski, Andrzej, Ołdziej, Stanislaw, Levitt, Michael, Scheraga, Harold, Seok, Chaok, Söding, Johannes, Vishveshwara, Saraswathi, Xu, Dong, & Crivelli, Silvia N. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. United States. https://doi.org/10.1038/s41598-018-26812-8
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Keasar, Chen, McGuffin, Liam J., Wallner, Björn, Chopra, Gaurav, Adhikari, Badri, Bhattacharya, Debswapna, Blake, Lauren, Bortot, Leandro Oliveira, Cao, Renzhi, Dhanasekaran, B. K., Dimas, Itzhel, Faccioli, Rodrigo Antonio, Faraggi, Eshel, Ganzynkowicz, Robert, Ghosh, Sambit, Ghosh, Soma, Giełdoń, Artur, Golon, Lukasz, He, Yi, Heo, Lim, Hou, Jie, Khan, Main, Khatib, Firas, Khoury, George A., Kieslich, Chris, Kim, David E., Krupa, Pawel, Lee, Gyu Rie, Li, Hongbo, Li, Jilong, Lipska, Agnieszka, Liwo, Adam, Maghrabi, Ali Hassan A., Mirdita, Milot, Mirzaei, Shokoufeh, Mozolewska, Magdalena A., Onel, Melis, Ovchinnikov, Sergey, Shah, Anand, Shah, Utkarsh, Sidi, Tomer, Sieradzan, Adam K., Ślusarz, Magdalena, Ślusarz, Rafal, Smadbeck, James, Tamamis, Phanourios, Trieber, Nicholas, Wirecki, Tomasz, Yin, Yanping, Zhang, Yang, Bacardit, Jaume, Baranowski, Maciej, Chapman, Nicholas, Cooper, Seth, Defelicibus, Alexandre, Flatten, Jeff, Koepnick, Brian, Popović, Zoran, Zaborowski, Bartlomiej, Baker, David, Cheng, Jianlin, Czaplewski, Cezary, Delbem, Alexandre Cláudio Botazzo, Floudas, Christodoulos, Kloczkowski, Andrzej, Ołdziej, Stanislaw, Levitt, Michael, Scheraga, Harold, Seok, Chaok, Söding, Johannes, Vishveshwara, Saraswathi, Xu, Dong, and Crivelli, Silvia N. Mon . "An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12". United States. https://doi.org/10.1038/s41598-018-26812-8. https://www.osti.gov/servlets/purl/1478361.
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@article{osti_1478361,
title = {An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12},
author = {Keasar, Chen and McGuffin, Liam J. and Wallner, Björn and Chopra, Gaurav and Adhikari, Badri and Bhattacharya, Debswapna and Blake, Lauren and Bortot, Leandro Oliveira and Cao, Renzhi and Dhanasekaran, B. K. and Dimas, Itzhel and Faccioli, Rodrigo Antonio and Faraggi, Eshel and Ganzynkowicz, Robert and Ghosh, Sambit and Ghosh, Soma and Giełdoń, Artur and Golon, Lukasz and He, Yi and Heo, Lim and Hou, Jie and Khan, Main and Khatib, Firas and Khoury, George A. and Kieslich, Chris and Kim, David E. and Krupa, Pawel and Lee, Gyu Rie and Li, Hongbo and Li, Jilong and Lipska, Agnieszka and Liwo, Adam and Maghrabi, Ali Hassan A. and Mirdita, Milot and Mirzaei, Shokoufeh and Mozolewska, Magdalena A. and Onel, Melis and Ovchinnikov, Sergey and Shah, Anand and Shah, Utkarsh and Sidi, Tomer and Sieradzan, Adam K. and Ślusarz, Magdalena and Ślusarz, Rafal and Smadbeck, James and Tamamis, Phanourios and Trieber, Nicholas and Wirecki, Tomasz and Yin, Yanping and Zhang, Yang and Bacardit, Jaume and Baranowski, Maciej and Chapman, Nicholas and Cooper, Seth and Defelicibus, Alexandre and Flatten, Jeff and Koepnick, Brian and Popović, Zoran and Zaborowski, Bartlomiej and Baker, David and Cheng, Jianlin and Czaplewski, Cezary and Delbem, Alexandre Cláudio Botazzo and Floudas, Christodoulos and Kloczkowski, Andrzej and Ołdziej, Stanislaw and Levitt, Michael and Scheraga, Harold and Seok, Chaok and Söding, Johannes and Vishveshwara, Saraswathi and Xu, Dong and Crivelli, Silvia N.},
abstractNote = {Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research.},
doi = {10.1038/s41598-018-26812-8},
journal = {Scientific Reports},
number = 1,
volume = 8,
place = {United States},
year = {Mon Jul 02 00:00:00 EDT 2018},
month = {Mon Jul 02 00:00:00 EDT 2018}
}
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