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

Author

Keasar, Chen, McGuffin, Liam J, Wallner, Björn, Chopra, Gaurav, Adhikari, Badri, Bhattacharya, Debswapna, Blake, Lauren, Bortot, Leandro Oliveira, Cao, Renzhi, Dhanasekaran, BK, 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, Foldit Players consortium, and Crivelli, Silvia N

Subjects
Foldit Players consortium, Humans, Caspases, Computational Biology, Protein Conformation, Models, Molecular, Software, Caspase 12, Models, Molecular, Biochemistry and Cell Biology, Other Physical Sciences
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.

Published
2018

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

Author

Keasar, C, McGuffin, LJ, Wallner, B, Chopra, G, Adhikari, B, Bhattacharya, D, Blake, L, Bortot, LO, Cao, R, Dhanasekaran, BK, Dimas, I, Faccioli, RA, Faraggi, E, Ganzynkowicz, R, Ghosh, S, Giełdoń, A, Golon, L, He, Y, Heo, L, Hou, J, Khan, M, Khatib, F, Khoury, GA, Kieslich, C, Kim, DE, Krupa, P, Lee, GR, Li, H, Li, J, Lipska, A, Liwo, A, Maghrabi, AHA, Mirdita, M, Mirzaei, S, Mozolewska, MA, Onel, M, Ovchinnikov, S, Shah, A, Shah, U, Sidi, T, Sieradzan, AK, Ślusarz, M, Ślusarz, R, Smadbeck, J, Tamamis, P, Trieber, N, Wirecki, T, Yin, Y, Zhang, Y, Bacardit, J, Baranowski, M, Chapman, N, Cooper, S, Defelicibus, A, Flatten, J, Koepnick, B, Popović, Z, Zaborowski, B, Baker, D, Cheng, J, Czaplewski, C, Delbem, ACB, Floudas, C, Kloczkowski, A, Ołdziej, S, Levitt, M, Scheraga, H, Seok, C, Söding, J, Vishveshwara, S, Xu, D, Caglar, A, Coral, A, MacMillan, A, Lubow, A, Failer, B, Kestemont, B, Landers, CR, Painter, CR, Garnier, C, Sellin, C, Janz, D, and Wheeler, DC

Abstract

© 2018 The Author(s). 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.

Published
2018

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

Author

Shah U, Lim Heo, Renzhi Cao, Chaok Seok, Gaurav Chopra, Soma Ghosh, Phanourios Tamamis, Maghrabi Aha, Sergey Ovchinnikov, Hailong Li, Chris A. Kieslich, Dhanasekaran Bk, Milot Mirdita, Rafał Ślusarz, Adam Liwo, Kim De, Gyu Rie Lee, Michael Levitt, James Smadbeck, Blake L, Adam K. Sieradzan, Seth Cooper, Andrzej Kloczkowski, Zoran Popović, Rodrigo Antonio Faccioli, Cezary Czaplewski, Yuxin Yin, Jie Hou, Brian Koepnick, Shah A, Jilong Li, Maciej Baranowski, Chen Keasar, Yang Zhang, Delbem Acb, Magdalena A. Mozolewska, Christodoulos A. Floudas, Agnieszka G. Lipska, Badri Adhikari, Yi He, Dimas I, Leandro Oliveira Bortot, Liam J. McGuffin, Paweł Krupa, Bartłomiej Zaborowski, David Baker, Alexandre Defelicibus, Eshel Faraggi, Melis Onel, Johannes Söding, Tomasz K Wirecki, Jeff Flatten, Jianlin Cheng, Firas Khatib, Dong Xu, Silvia Crivelli, Stanisław Ołdziej, Saraswathi Vishveshwara, Debswapna Bhattacharya, Golon L, George A. Khoury, Harold A. Scheraga, Artur Giełdoń, Jaume Bacardit, Chapman N, Björn Wallner, Shokoufeh Mirzaei, Khan M, Magdalena J. Ślusarz, Tomer Sidi, Trieber N, and Robert Ganzynkowicz

Subjects
Models, Molecular, 0301 basic medicine, Computer science, SISTEMAS EMBUTIDOS, Protein Conformation, Science, Article, Field (computer science), Annan data- och informationsvetenskap, Foldit Players consortium, 03 medical and health sciences, Protein structure, Models, Humans, CASP, Caspase 12, Multidisciplinary, Computational Biology, Molecular, Protein structure prediction, Data science, Test (assessment), Other Physical Sciences, 030104 developmental biology, Scale (social sciences), Caspases, Medicine, Biochemistry and Cell Biology, Other Computer and Information Science, Software
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. Funding Agencies|Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Science Undergraduate Laboratory Internship (SULI) program; U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Visiting Faculty Program (VFP); United States-Israel Binational Science Foundation (BSF) [2009432]; Israel Science Foundation (ISF) [1122/14]; National Institute of General Medical Sciences [R01GM093123, GM083107, GM116960]; Purdue University start-up funds; Ralph W. and Grace M. Showalter Trust Award; Jim and Diann Robbers Cancer Research Grant for New Investigators Award; Brazilian agency: FAPESP; Brazilian agency: CAPES; Brazilian agency: CNPq; NIH [GM-14312]; NSF [MCB-10-19767]; National Institutes of Medicine [GM11574901]; Swedish Research Council [2012-5270, 2016-05369]; Swedish e-Science Research Center; Polish National Science Center [UMO-2013/10/M/ST4/00640]; IISc Mathematical Initiative Assistantship; National Academy of Sciences, India; National Institutes of Health [R01-GM100701, R01GM052032]; National Science Foundation; National Science Foundation Graduate Research Fellowship [DGE-1148900]; Princeton Institute for Computational Science and Engineering (PICSciE); Princeton University Office of Information Technology; UK Engineering and Physical Sciences Research Council [EP/M020576/1, EP/N031962/1]; National Research Foundation of Korea [2016R1A2A1A05005485]

Published
2018

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