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

07/02/2018

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

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: Chen Keasar - Ben-Gurion University of the Negev
Liam J. McGuffin - University of Reading
Bjorn Wallner - Linköping University
Gaurav Chopra - Purdue University West Lafayette
Badri Adhikari - University of Missouri
Debswapna Bhattacharya - University of Missouri
Lauren Blake - Lawrence Berkeley National Laboratory
Leandro Oliveira Bortot - Universidade de São Paulo
Renzhi Cao - University of Missouri
B. K. Dhanasekaran - Indian Institute of Science Bangalore
Itzhel Dimas - Lawrence Berkeley National Laboratory
Rodrigo Antonio Faccioli - Universidade de São Paulo
Eshel Faraggi - Nationwide Children's Hospital
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 - University of California, Merced
Lim Heo - Seoul National University
Jie Hou - University of Missouri
Main Khan - University of Massachusetts Dartmouth
Firas Khatib - University of Massachusetts Dartmouth
George A. Khoury - Princeton University
Chris Kieslich - Texas A&M University
David E. Kim - University of Washington
Pawel Krupa - University of Gdańsk
Gyu Rie Lee - Seoul National University
Hongbo Li - University of Missouri
Jilong Li - University of Missouri
Agnieszka Lipska - University of Gdańsk
Adam Liwo - University of Gdańsk
Ali Hassan A. Maghrabi - University of Reading
Milot Mirdita - Max Planck Institute for Biophysical Chemistry
Shokoufeh Mirzaei - Lawrence Berkeley National Laboratory
Magdalena A. Mozolewska - University of Gdańsk
Melis Onel - Texas A&M University
Sergey Ovchinnikov - University of Washington
Anand Shah - University of Massachusetts Dartmouth
Utkarsh Shah - Texas A&M University
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 University
Nicholas Trieber - University of Massachusetts Dartmouth
Tomasz Wirecki - University of Gdańsk
Yanping Yin - Cornell University
Yang Zhang - University of Michigan–Ann Arbor
Jaume Bacardit - Newcastle University
Maciej Baranowski - Gdańsk Medical University
Nicholas Chapman - University of Washington
Seth Cooper - Northeastern University
Alexandre Defelicibus - Universidade de São Paulo
Jeff Flatten - University of Washington
Brian Koepnick - University of Washington
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 University
Andrzej Kloczkowski - University of Gdańsk
Stanislaw Oldziej - University of Gdańsk
Michael Levitt - Stanford University
Harold Scheraga - Cornell University
Chaok Seok - Seoul National University
Johannes Soeding - Max
Saraswathi Vishveshwara - Indian Institute of Science Bangalore
Dong Xu - University of Missouri
Silvia N. Crivelli - University of California, Davis
Foldit Players Consortium
Publication Details: Scientific reports, Vol.8(Jul (E-published)), pp.9939-18
Publisher: NATURE PORTFOLIO
Number of pages: 18
Language: English
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 2016-05369 / Swedish Research Council 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 2012-5270; 2016-05369 / Swedish Research Council 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)
Academic Unit: Department of Computer and Information Science
Resource Type: Journal article
DOI: https://doi.org/10.1038/s41598-018-26812-8
Record Identifier: 9914443222901301