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

Chen Keasar , Liam J. Mcguffin , Björn Wallner , Gaurav Chopra , Badri Adhikari , Debswapna Bhattacharya , Lauren 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 A. Khoury , Chris Kieslich , David E. Kim , Paweł Krupa , Gyu Rie Lee , Hongbo Li , Jilong Li , Agnieszka Lipska , Adam Liwo , Ali Hassan A. Maghrabi , Milot Mirdita , Shokoufeh Mirzaei , Magdalena Mozolewska , Melis Onel , Sergey Ovchinnikov , Anand Shah , Utkarsh Shah , Tomer Sidi , Adam Sieradzan , Magdalena Ślusarz , Rafał Ślusarz , James 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 Cláudio Botazzo Delbem , Christodoulos Floudas , Andrzej Kloczkowski , Stanisław Ołdziej , Michael Levitt , Harold Scheraga , Chaok Seok , Johannes Soeding , Saraswathi Vishveshwara , Dong Xu , Silvia N. Crivelli

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.
Author Chen Keasar
Chen Keasar,,
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, Liam J. Mcguffin
Liam J. Mcguffin,,
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, Björn Wallner
Björn Wallner,,
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, Gaurav Chopra
Gaurav Chopra,,
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, Badri Adhikari
Badri Adhikari,,
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, Debswapna Bhattacharya
Debswapna Bhattacharya,,
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, Lauren Blake
Lauren Blake,,
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, Leandro Oliveira Bortot
Leandro Oliveira Bortot,,
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, Renzhi Cao
Renzhi Cao,,
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, B. K. Dhanasekaran
B. K. Dhanasekaran,,
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et al.`
Journal seriesScientific Reports, ISSN 2045-2322, (A 40 pkt)
Issue year2018
Vol8
Pages1-18
Publication size in sheets0.85
DOIDOI:10.1038/s41598-018-26812-8
URL https://www.nature.com/articles/s41598-018-26812-8.pdf
Languageen angielski
LicenseJournal (articles only); published final; Uznanie Autorstwa (CC-BY); with publication
Score (nominal)40
ScoreMinisterial score = 40.0, 26-10-2018, ArticleFromJournal
Ministerial score (2013-2016) = 40.0, 26-10-2018, ArticleFromJournal
Publication indicators WoS Impact Factor: 2016 = 4.259 (2) - 2016=4.847 (5)
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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.
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