Scientific Reports (Jul 2018)
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,
- 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,
- Jaume Bacardit,
- Maciej Baranowski,
- Nicholas Chapman,
- Seth Cooper,
- Alexandre Defelicibus,
- Jeff Flatten,
- Brian Koepnick,
- Zoran Popović,
- Bartlomiej Zaborowski,
- David Baker,
- Jianlin Cheng,
- Cezary Czaplewski,
- Alexandre Cláudio Botazzo Delbem,
- Christodoulos Floudas,
- Andrzej Kloczkowski,
- Stanislaw Ołdziej,
- Michael Levitt,
- Harold Scheraga,
- Chaok Seok,
- Johannes Söding,
- Saraswathi Vishveshwara,
- Dong Xu,
- Foldit Players consortium,
- Silvia N. Crivelli
Affiliations
- Chen Keasar
- Department of Computer Science, Ben Gurion University of the Negev
- Liam J. McGuffin
- Biomedical Sciences Division, School of Biological Sciences, University of Reading
- Björn Wallner
- Division of Bioinformatics, Department of Physics, Chemistry, and Biology, Linköping University
- Gaurav Chopra
- Department of Chemistry, College of Science, Purdue University
- Badri Adhikari
- Department of Electrical Engineering and Computer Science, University of Missouri
- Debswapna Bhattacharya
- Department of Electrical Engineering and Computer Science, University of Missouri
- Lauren Blake
- Lawrence Berkeley National Laboratory
- Leandro Oliveira Bortot
- Laboratory of Biological Physics, Faculty of Pharmaceutical Sciences at Ribeirão Preto, University of São Paulo
- Renzhi Cao
- Department of Electrical Engineering and Computer Science, University of Missouri
- B. K. Dhanasekaran
- Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science
- Itzhel Dimas
- Lawrence Berkeley National Laboratory
- Rodrigo Antonio Faccioli
- Institute of Mathematical and Computer Sciences, University of São Paulo
- Eshel Faraggi
- Research and Information Systems, LLC
- Robert Ganzynkowicz
- Faculty of Chemistry, University of Gdansk
- Sambit Ghosh
- Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science
- Soma Ghosh
- Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science
- Artur Giełdoń
- Faculty of Chemistry, University of Gdansk
- Lukasz Golon
- Faculty of Chemistry, University of Gdansk
- Yi He
- School of Engineering, University of California
- Lim Heo
- Department of Chemistry, Seoul National University
- Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri
- Main Khan
- Department of Computer and Information Science, University of Massachusetts Dartmouth
- Firas Khatib
- Department of Computer and Information Science, University of Massachusetts Dartmouth
- George A. Khoury
- Department of Chemical and Biological Engineering, Princeton University
- Chris Kieslich
- Texas A&M Energy Institute, Texas A&M University
- David E. Kim
- Department of Biochemistry, University of Washington
- Pawel Krupa
- Faculty of Chemistry, University of Gdansk
- Gyu Rie Lee
- Department of Chemistry, Seoul National University
- Hongbo Li
- Department of Electrical Engineering and Computer Science, University of Missouri
- Jilong Li
- Department of Electrical Engineering and Computer Science, University of Missouri
- Agnieszka Lipska
- Faculty of Chemistry, University of Gdansk
- Adam Liwo
- Faculty of Chemistry, University of Gdansk
- Ali Hassan A. Maghrabi
- Biomedical Sciences Division, School of Biological Sciences, University of Reading
- Milot Mirdita
- Max Planck Institute for Biophysical Chemistry
- Shokoufeh Mirzaei
- Lawrence Berkeley National Laboratory
- Magdalena A. Mozolewska
- Faculty of Chemistry, University of Gdansk
- Melis Onel
- Artie McFerrin Department of Chemical Engineering, Texas A&M University
- Sergey Ovchinnikov
- Department of Biochemistry, University of Washington
- Anand Shah
- Department of Computer and Information Science, University of Massachusetts Dartmouth
- Utkarsh Shah
- Artie McFerrin Department of Chemical Engineering, Texas A&M University
- Tomer Sidi
- Department of Computer Science, Ben Gurion University of the Negev
- Adam K. Sieradzan
- Faculty of Chemistry, University of Gdansk
- Magdalena Ślusarz
- Faculty of Chemistry, University of Gdansk
- Rafal Ślusarz
- Faculty of Chemistry, University of Gdansk
- James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University
- Phanourios Tamamis
- Texas A&M Energy Institute, Texas A&M University
- Nicholas Trieber
- Department of Computer and Information Science, University of Massachusetts Dartmouth
- Tomasz Wirecki
- Faculty of Chemistry, University of Gdansk
- Yanping Yin
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University
- Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan
- Jaume Bacardit
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing, Newcastle University
- Maciej Baranowski
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk
- Nicholas Chapman
- Center for Game Science, Department of Computer Science & Engineering, University of Washington
- Seth Cooper
- College of Computer and Information Science, Northeastern University
- Alexandre Defelicibus
- Institute of Mathematical and Computer Sciences, University of São Paulo
- Jeff Flatten
- Center for Game Science, Department of Computer Science & Engineering, University of Washington
- Brian Koepnick
- Department of Biochemistry, University of Washington
- Zoran Popović
- Center for Game Science, Department of Computer Science & Engineering, University of Washington
- Bartlomiej Zaborowski
- Faculty of Chemistry, University of Gdansk
- David Baker
- Department of Biochemistry, University of Washington
- Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri
- Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk
- Alexandre Cláudio Botazzo Delbem
- Institute of Mathematical and Computer Sciences, University of São Paulo
- Christodoulos Floudas
- Texas A&M Energy Institute, Texas A&M University
- Andrzej Kloczkowski
- Faculty of Chemistry, University of Gdansk
- Stanislaw Ołdziej
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk
- Michael Levitt
- Department of Structural Biology, School of Medicine, Stanford University
- Harold Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University
- Chaok Seok
- Department of Chemistry, Seoul National University
- Johannes Söding
- Max Planck Institute for Biophysical Chemistry
- Saraswathi Vishveshwara
- Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science
- Dong Xu
- Department of Electrical Engineering and Computer Science, University of Missouri
- Foldit Players consortium
- Silvia N. Crivelli
- Lawrence Berkeley National Laboratory
- DOI
- https://doi.org/10.1038/s41598-018-26812-8
- Journal volume & issue
-
Vol. 8,
no. 1
pp. 1 – 18
Abstract
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.
