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

被引:0
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作者
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
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 Ślusarz
Rafal Ślusarz
James Smadbeck
Phanourios Tamamis
Nicholas Trieber
Tomasz Wirecki
Yanping Yin
Yang Zhang
机构
[1] Ben Gurion University of the Negev,Department of Computer Science
[2] University of Reading,Biomedical Sciences Division, School of Biological Sciences
[3] Linköping University,Division of Bioinformatics, Department of Physics, Chemistry, and Biology
[4] Purdue University,Department of Chemistry, College of Science
[5] Purdue University,Purdue Institute for Drug Discovery
[6] Purdue University,Purdue Center for Cancer Research
[7] Purdue University,Purdue Institute for Inflammation, Immunology and Infectious Disease
[8] Purdue University,Purdue Institute for Integrative Neuroscience
[9] University of Missouri,Department of Electrical Engineering and Computer Science
[10] Auburn University,Department of Computer Science and Software Engineering
[11] Lawrence Berkeley National Laboratory,Laboratory of Biological Physics, Faculty of Pharmaceutical Sciences at Ribeirão Preto
[12] University of São Paulo,Molecular Biophysics Unit and IISC Mathematics Initiative
[13] Indian Institute of Science,Institute of Mathematical and Computer Sciences
[14] University of São Paulo,Research and Information Systems
[15] LLC,Department of Biochemistry and Molecular Biology
[16] IU School of Medicine,Batelle Center for Mathematical Medicine
[17] The Research Institute at Nationwide Children’s Hospital,Faculty of Chemistry
[18] University of Gdansk,School of Engineering
[19] University of California,Department of Chemistry
[20] Seoul National University,Department of Computer and Information Science
[21] University of Massachusetts Dartmouth,Department of Chemical and Biological Engineering
[22] Princeton University,Texas A&M Energy Institute
[23] Texas A&M University,Department of Biochemistry
[24] University of Washington,Howard Hughes Medical Institute
[25] University of Washington,School of Computer Science and Information Technology
[26] NorthEast Normal University,Christopher S. Bond Life Sciences Center
[27] University of Missouri,Artie McFerrin Department of Chemical Engineering
[28] Max Planck Institute for Biophysical Chemistry,Institute for Protein Design
[29] California State Polytechnic University,Baker Laboratory of Chemistry and Chemical Biology
[30] Texas A&M University,Department of Computational Medicine and Bioinformatics
[31] University of Washington,Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing
[32] Cornell University,Intercollegiate Faculty of Biotechnology
[33] University of Michigan,Center for Game Science, Department of Computer Science & Engineering
[34] Newcastle University,College of Computer and Information Science
[35] University of Gdańsk and Medical University of Gdańsk,Department of Structural Biology, School of Medicine
[36] University of Washington,Department of Computer Science
[37] Northeastern University,Rosetta Commons
[38] Stanford University,undefined
[39] University of California,undefined
[40] University of Washington,undefined
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摘要
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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