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

Chen Keasar; Liam J. McGuffin; Bjorn 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 Gieldon; Lukasz Golon; Yi He; Lim Heo; Jie Hou; Main Khan; Firas Khatib; George A. Khoury; Chris Kieslich; David E. Kim; Pawel Krupa; Gyu Rie Lee; Hongbo Li; Jilong Li; Agnieszka Lipska; Adam Liwo; Ali Hassan A. Maghrabi; Milot Mirdita; Shokoufeh Mirzaei; Magdalena A. Mozolewska; Melis Onel; Sergey Ovchinnikov; Anand Shah; Utkarsh Shah; Tomer Sidi; Adam K. Sieradzan; Magdalena Slusarz; Rafal Slusarz; 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 Popovic; Bartlomiej Zaborowski; David Baker; Jianlin Cheng; Cezary Czaplewski; Alexandre Claudio Botazzo Delbem; Christodoulos Floudas; Andrzej Kloczkowski; Stanislaw Oldziej; Michael Levitt; Harold Scheraga; Chaok Seok; Johannes Soeding; Saraswathi Vishveshwara; Dong Xu; Silvia N. Crivelli; Foldit Players Consortium

doi:10.1038/s41598-018-26812-8

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

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

Chen Keasar, Liam J. McGuffin, Bjorn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren Blake, Leandro Oliveira Bortot, Renzhi Cao, B. K. Dhanasekaran, …

Scientific reports, Vol.8(Jul (E-published)), pp.9939-18

02/07/2018

DOI: https://doi.org/10.1038/s41598-018-26812-8

PMCID: PMC6028396

PMID: 29967418

Abstract

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

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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Title: An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
Creators - without role: Chen Keasar - Ben-Gurion University of the Negev
Liam J. McGuffin - University of Reading
Bjorn Wallner - Linköping University
Gaurav Chopra - Purdue Univ, Dept Chem, Coll Sci, W Lafayette, IN 47907 USA
Badri Adhikari - University of Missouri
Debswapna Bhattacharya - Auburn University
Lauren Blake - Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA
Leandro Oliveira Bortot - Univ Sao Paulo, Lab Biol Phys, Fac Pharmaceut Sci Ribeirao Preto, Sao Paulo, Brazil
Renzhi Cao - University of Missouri
B. K. Dhanasekaran - Indian Institute of Science Bangalore
Itzhel Dimas - Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA
Rodrigo Antonio Faccioli - Univ Sao Paulo, Inst Math & Comp Sci, Sao Paulo, Brazil
Eshel Faraggi - Product Innovation and Engineering (United States, Saint James) - LLC
Robert Ganzynkowicz - University of Gdańsk
Sambit Ghosh - Indian Institute of Science Bangalore
Soma Ghosh - Indian Institute of Science Bangalore
Artur Gieldon - University of Gdańsk
Lukasz Golon - University of Gdańsk
Yi He - Supreme Council Of Health
Lim Heo - Seoul Natl Univ, Dept Chem, Seoul, South Korea
Jie Hou - University of Missouri
Main Khan - Univ Massachusetts, Dept Comp & Informat Sci, Dartmouth, MA USA
Firas Khatib - Univ Massachusetts, Dept Comp & Informat Sci, Dartmouth, MA USA
George A. Khoury - Princeton University
Chris Kieslich - Texas A&M Univ, Texas A&M Energy Inst, College Stn, TX USA
David E. Kim - University of Washington
Pawel Krupa - University of Gdańsk
Gyu Rie Lee - Seoul Natl Univ, Dept Chem, Seoul, South Korea
Hongbo Li - University of Missouri
Jilong Li - University of Missouri
Agnieszka Lipska - University of Gdańsk
Adam Liwo - University of Gdańsk
Ali Hassan A. Maghrabi
Milot Mirdita - Max
Shokoufeh Mirzaei - Calif State Polytech Univ Pomona, Pomona, CA 91768 USA
Magdalena A. Mozolewska - University of Gdańsk
Melis Onel - Texas A&M Univ, Artie McFerrin Dept Chem Engn, College Stn, TX USA
Sergey Ovchinnikov - University of Washington
Anand Shah - Univ Massachusetts, Dept Comp & Informat Sci, Dartmouth, MA USA
Utkarsh Shah - Texas A&M Univ, Artie McFerrin Dept Chem Engn, College Stn, TX USA
Tomer Sidi - Ben-Gurion University of the Negev
Adam K. Sieradzan - University of Gdańsk
Magdalena Slusarz - University of Gdańsk
Rafal Slusarz - University of Gdańsk
James Smadbeck - Princeton University
Phanourios Tamamis - Texas A&M Univ, Artie McFerrin Dept Chem Engn, College Stn, TX USA
Nicholas Trieber - Univ Massachusetts, Dept Comp & Informat Sci, Dartmouth, MA USA
Tomasz Wirecki - University of Gdańsk
Yanping Yin - Cornell University
Yang Zhang - College Station Medical Center
Jaume Bacardit - Newcastle Univ, Sch Comp, Interdisciplinary Comp & Complex BioSyst ICOS Res, Newcastle Upon Tyne, Tyne & Wear, England
Maciej Baranowski - University of Gdańsk
Nicholas Chapman - University of Washington
Seth Cooper - Northeastern Univ, Coll Comp & Informat Sci, Boston, MA 02115 USA
Alexandre Defelicibus - Univ Sao Paulo, Inst Math & Comp Sci, Sao Paulo, Brazil
Jeff Flatten - University of Washington
Brian Koepnick
Zoran Popovic - University of Washington
Bartlomiej Zaborowski - University of Gdańsk
David Baker - University of Washington
Jianlin Cheng - University of Missouri
Cezary Czaplewski - University of Gdańsk
Alexandre Claudio Botazzo Delbem - Univ Sao Paulo, Inst Math & Comp Sci, Sao Paulo, Brazil
Christodoulos Floudas - Texas A&M Univ, Texas A&M Energy Inst, College Stn, TX USA
Andrzej Kloczkowski - University of Gdańsk
Stanislaw Oldziej - University of Gdańsk
Michael Levitt - Stanford University
Harold Scheraga - Cornell University
Chaok Seok
Johannes Soeding - Max
Saraswathi Vishveshwara
Dong Xu
Silvia N. Crivelli - Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA
Foldit Players Consortium
Publication Details: Scientific reports, Vol.8(Jul (E-published)), pp.9939-18
Publisher: Springer Nature
Number of pages: 18
Grant note: Ralph W. and Grace M. Showalter Trust Award Brazilian agency: FAPESP; Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) Purdue University start-up funds GM11574901 / National Institutes of Medicine 1122/14 / Israel Science Foundation (ISF); Israel Science Foundation Jim and Diann Robbers Cancer Research Grant for New Investigators Award GM-14312 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA EP/M020576/1; EP/N031962/1 / UK Engineering and Physical Sciences Research Council; UK Research & Innovation (UKRI); Engineering & Physical Sciences Research Council (EPSRC) Brazilian agency: CAPES; Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES) Princeton Institute for Computational Science and Engineering (PICSciE) 2016R1A2A1A05005485 / National Research Foundation of Korea National Academy of Sciences, India; Department of Science & Technology (India) R01-GM100701; R01GM052032 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA DGE-1148900 / National Science Foundation Graduate Research Fellowship; National Science Foundation (NSF) R01GM093123; GM083107; GM116960 / National Institute of General Medical Sciences; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) MCB-10-19767 / NSF; National Science Foundation (NSF) 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; United States Department of Energy (DOE) Swedish e-Science Research Center 2009432 / United States-Israel Binational Science Foundation (BSF); US-Israel Binational Science Foundation 2012-5270; 2016-05369 / Swedish Research Council; Swedish Research Council for Health Working Life & Welfare (Forte); Swedish Research Council Formas EP/M020576/1; EP/N031962/1 / EPSRC; UK Research & Innovation (UKRI); Engineering & Physical Sciences Research Council (EPSRC) Brazilian agency: CNPq; Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ) 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 Department of Energy (DOE) National Science Foundation; National Science Foundation (NSF) Princeton University Office of Information Technology; Princeton University DE-AC02-05CH11231 / Office of Science of the U.S. Department of Energy; United States Department of Energy (DOE) UMO-2013/10/M/ST4/00640 / Polish National Science Center IISc Mathematical Initiative Assistantship
Identifiers: 9931438708331
Academic Unit: Umm Al Qura University
Language: English
Resource Type: Journal article