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

2018; Nature Portfolio; Volume: 8; Issue: 1 Linguagem: Inglês

10.1038/s41598-018-26812-8

2045-2322

Chen Keasar, Liam J. McGuffin, Björn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren A. Blake, Leandro Oliveira Bortot, Renzhi Cao, B. K. Dhanasekaran, Itzhel Dimas, Rodrigo Antonio Faccioli, Eshel Faraggi, Robert Ganzynkowicz, Sambit Ghosh, Soma Ghosh, Artur Giełdoń, Łukasz Golon, Yi He, Lim Heo, Jie Hou, Main Khan, Firas Khatib, George Khoury, Chris A. Kieslich, David E. Kim, Paweł Krupa, Gyu Rie Lee, Hongbo Li, Jilong Li, Agnieszka G. Lipska, Adam Liwo, Ali H. A. Maghrabi, Milot Mirdita, Shokoufeh Mirzaei, Magdalena A. Mozolewska, Melis Onel, Sergey Ovchinnikov, Anand S. Shah, Utkarsh Shah, Tomer Sidi, Adam K. Sieradzan, Magdalena J. Ślusarz, Rafał Ślusarz, James B. Smadbeck, Phanourios Tamamis, Nicholas Trieber, Tomasz Wirecki, Yanping Yin, Yang Zhang, Jaume Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Brian Koepnick, Zoran Popović, Bartłomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Alexandre C. B. Delbem, Christodoulos A. Floudas, Andrzej Kloczkowski, Stanisław Ołdziej, Michael Levitt, Harold A. Scheraga, Chaok Seok, Johannes Söding, Saraswathi Vishveshwara, Dong Xu, Ahmet Çağlar, Alan Coral, Alison MacMillan, Allen Lubow, Barbara Failer, Bruno Kestemont, Catherine R. Landers, Charles Robert Painter, Christophe Garnier, Claudine Sellin, Dietmar Janz, Douglas Craig Wheeler, Vera Simon, Dylan M. Flear, Emmanuel Croze, George Victor McIlvaine, Gil Beecher, Gordon Lawrie, Guy Ykman, Harald Feldmann, Heidemarie K. Fuentes, Hosokawa Terumasa, Istvan Kovanecz, James Absalom Longino, Jan Hendrik Nijland, Jasper A. Diderich, Jeffrey M. Canfield, Jesper Eriksson, Jesse Slone, J. Appel, Joanne Mitchell, John H. Mitch, Jorn Loots-Boiy, June M. Brownlee, Karsten Wilson, Keith Clayton, Kenneth E. DeFord, Kirk J. Abbey, Larry C. Withers, Linda Wei, Lloyd Ives, Lori Anne Miller, L. A. Carpenter, Manasa G. Sharma, Manuel Ricci, Mark Stewart Binfield, Matthew John Davids, Matthias Gaebel, Michael D. Cassidy, Michael Fagiola, Michael Pfützenreuter, Nova Barlow, Peter John Triggiani, Renton Braden Mathew Innes, Robert Leduc, Rodrigo Luccas Corrêa dos Santos Gomes, Rosemarie L. R. Morneau, Scott J. Zaccanelli, Susan C. Kleinfelter, T. J. A. van der Laan, Thomas Bausewein, Thomas J. George, Varichev Mikhail, Walter Barmettler, Silvia Crivelli,

Mass Spectrometry Techniques and Applications

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.