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

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Keasar, ChenBen Gurion Univ Negev, Israel (author)

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

Article/chapterEnglish2018

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2018-07-02
NATURE PUBLISHING GROUP,2018
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LIBRIS-ID:oai:DiVA.org:liu-149683
https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-149683URI
https://doi.org/10.1038/s41598-018-26812-8DOI

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Language:English
Summary in:English

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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]
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.

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McGuffin, Liam J.Univ Reading, England (author)
Wallner, Björn,1975-Linköpings universitet,Bioinformatik,Tekniska fakulteten(Swepub:liu)bjowa51 (author)
Chopra, GauravPurdue Univ, IN USA (author)
Adhikari, BadriUniv Missouri, MO USA (author)
Bhattacharya, DebswapnaAuburn Univ, AL 36849 USA (author)
Blake, LaurenLawrence Berkeley Natl Lab, CA 94720 USA (author)
Bortot, Leandro OliveiraUniv Sao Paulo, Brazil (author)
Cao, RenzhiUniv Missouri, MO USA (author)
Dhanasekaran, B. K.Indian Inst Sci, India (author)
Dimas, ItzhelLawrence Berkeley Natl Lab, CA 94720 USA (author)
Faccioli, Rodrigo AntonioUniv Sao Paulo, Brazil (author)
Faraggi, EshelRes and Informat Syst LLC, CA USA; IU Sch Med, IN USA; Nationwide Childrens Hosp, OH USA (author)
Ganzynkowicz, RobertUniv Gdansk, Poland (author)
Ghosh, SambitIndian Inst Sci, India (author)
Ghosh, SomaIndian Inst Sci, India (author)
Gieldon, ArturUniv Gdansk, Poland (author)
Golon, LukaszUniv Gdansk, Poland (author)
He, YiUniv Calif, CA USA (author)
Heo, LimSeoul Natl Univ, South Korea (author)
Hou, JieUniv Missouri, MO USA (author)
Khan, MainUniv Massachusetts, MA USA (author)
Khatib, FirasUniv Massachusetts, MA USA (author)
Khoury, George A.Princeton Univ, NJ 08544 USA (author)
Kieslich, ChrisTexas AandM Univ, TX USA (author)
Kim, David E.Univ Washington, WA 98195 USA; Univ Washington, WA 98195 USA (author)
Krupa, PawelUniv Gdansk, Poland (author)
Lee, Gyu RieSeoul Natl Univ, South Korea (author)
Li, HongboUniv Missouri, MO USA; NorthEast Normal Univ, Peoples R China; Univ Missouri, MO USA (author)
Li, JilongUniv Missouri, MO USA (author)
Lipska, AgnieszkaUniv Gdansk, Poland (author)
Liwo, AdamUniv Gdansk, Poland (author)
Maghrabi, Ali Hassan A.Univ Reading, England (author)
Mirdita, MilotMax Planck Inst Biophys Chem, Germany (author)
Mirzaei, ShokoufehCalif State Polytech Univ Pomona, CA 91768 USA (author)
Mozolewska, Magdalena A.Univ Gdansk, Poland (author)
Onel, MelisTexas AandM Univ, TX USA (author)
Ovchinnikov, SergeyUniv Washington, WA 98195 USA (author)
Shah, AnandUniv Massachusetts, MA USA (author)
Shah, UtkarshTexas AandM Univ, TX USA (author)
Sidi, TomerBen Gurion Univ Negev, Israel (author)
Sieradzan, Adam K.Univ Gdansk, Poland (author)
Slusarz, MagdalenaUniv Gdansk, Poland (author)
Slusarz, RafalUniv Gdansk, Poland (author)
Smadbeck, JamesPrinceton Univ, NJ 08544 USA (author)
Tamamis, PhanouriosTexas AandM Univ, TX USA (author)
Trieber, NicholasUniv Massachusetts, MA USA (author)
Wirecki, TomaszUniv Gdansk, Poland (author)
Yin, YanpingCornell Univ, NY USA (author)
Zhang, YangUniv Michigan, MI 48109 USA (author)
Bacardit, JaumeNewcastle Univ, England (author)
Baranowski, MaciejUniv Gdansk, Poland; Med Univ Gdansk, Poland (author)
Chapman, NicholasUniv Washington, WA 98195 USA (author)
Cooper, SethNortheastern Univ, MA 02115 USA (author)
Defelicibus, AlexandreUniv Sao Paulo, Brazil (author)
Flatten, JeffUniv Washington, WA 98195 USA (author)
Koepnick, BrianUniv Washington, WA 98195 USA (author)
Popovic, ZoranUniv Washington, WA 98195 USA (author)
Zaborowski, BartlomiejUniv Gdansk, Poland (author)
Baker, DavidUniv Washington, WA 98195 USA (author)
Cheng, JianlinUniv Missouri, MO USA (author)
Czaplewski, CezaryUniv Gdansk, Poland (author)
Botazzo Delbem, Alexandre ClaudioUniv Sao Paulo, Brazil (author)
Floudas, ChristodoulosTexas AandM Univ, TX USA (author)
Kloczkowski, AndrzejUniv Gdansk, Poland (author)
Oldziej, StanislawUniv Gdansk, Poland; Med Univ Gdansk, Poland (author)
Levitt, MichaelStanford Univ, CA 94305 USA (author)
Scheraga, HaroldCornell Univ, NY USA (author)
Seok, ChaokSeoul Natl Univ, South Korea (author)
Soeding, JohannesMax Planck Inst Biophys Chem, Germany (author)
Vishveshwara, SaraswathiIndian Inst Sci, India (author)
Xu, DongUniv Missouri, MO USA (author)
Crivelli, Silvia N.Lawrence Berkeley Natl Lab, CA 94720 USA; Univ Calif Davis, CA 95616 USA (author)
Ben Gurion Univ Negev, IsraelUniv Reading, England (creator_code:org_t)

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By the author/editor: Keasar, Chen; McGuffin, Liam J ...; Wallner, Björn, ...; Chopra, Gaurav; Adhikari, Badri; Bhattacharya, De ...; show more...; Blake, Lauren; Bortot, Leandro ...; Cao, Renzhi; Dhanasekaran, B. ...; Dimas, Itzhel; Faccioli, Rodrig ...; Faraggi, Eshel; Ganzynkowicz, Ro ...; Ghosh, Sambit; Ghosh, Soma; Gieldon, 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, Agnieszk ...; Liwo, Adam; Maghrabi, Ali Ha ...; Mirdita, Milot; Mirzaei, Shokouf ...; Mozolewska, Magd ...; Onel, Melis; Ovchinnikov, Ser ...; Shah, Anand; Shah, Utkarsh; Sidi, Tomer; Sieradzan, Adam ...; Slusarz, Magdale ...; Slusarz, Rafal; Smadbeck, James; Tamamis, Phanour ...; Trieber, Nichola ...; Wirecki, Tomasz; Yin, Yanping; Zhang, Yang; Bacardit, Jaume; Baranowski, Maci ...; Chapman, Nichola ...; Cooper, Seth; Defelicibus, Ale ...; Flatten, Jeff; Koepnick, Brian; Popovic, Zoran; Zaborowski, Bart ...; Baker, David; Cheng, Jianlin; Czaplewski, Ceza ...; Botazzo Delbem, ...; Floudas, Christo ...; Kloczkowski, And ...; Oldziej, Stanisl ...; Levitt, Michael; Scheraga, Harold; Seok, Chaok; Soeding, Johanne ...; Vishveshwara, Sa ...; Xu, Dong; Crivelli, Silvia ...; show less...

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