An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
Authors: 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 ,   Foldit Players consortium, Caglar Ahmet , Coral Alan , MacMillan Alison , Lubow Allen , Failer Barbara , Kestemont Bruno , Landers Catherine R. , Painter Charles Robert , Garnier Christophe , Sellin Claudine , Janz Dietmar , Wheeler Douglas Craig , Simon Vera , Flear Dylan M. , Croze Emmanuel , McIlvaine George Victor , Beecher Gil , Lawrie Gordon , Ykman Guy , Feldmann Harald , Fuentes Heidemarie K. , Terumasa Hosokawa , Kovanecz Istvan , Longino James Absalom , Nijland Jan Hendrik , Diderich Jasper A. , Canfield Jeffrey M. , Eriksson Jesper , Slone Jesse David , Appel Joan Goldsworthy , Mitchell Joanne , Mitch John , Loots-Boiy Jorn , Brownlee June M. , Wilson Karsten , Clayton Keith T. , DeFord Kenneth E. , Abbey Kirk J. , Withers Larry , Wei Linda , Ives Lloyd , Miller Lori A. , Carpenter Lynn , Sharma Manasa G. , Ricci Manuel , Binfield Mark Stewart , Davids Matthew John , Gaebel Matthias , Cassidy Michael D. , Fagiola Michael , Pfützenreuter Michael , Barlow Nova , Triggiani Peter John , Innes Renton Braden Mathew , Leduc Robert , dos Santos Gomes Rodrigo Luccas Corrêa , Morneau Rosemarie L. R. , Zaccanelli Scott J. , Kleinfelter Susan C. , van der Laan T. J. A. , Bausewein Thomas , George Thomas J. , Mikhail Varichev , Barmettler Walter , Crivelli Silvia N. 
Published: June 2018

AbstractEvery 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.