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

Autor: Keasar C; Department of Computer Science, Ben Gurion University of the Negev, Be'er sheva, Israel., McGuffin LJ; Biomedical Sciences Division, School of Biological Sciences, University of Reading, Reading, RG6 6AS, UK., Wallner B; Division of Bioinformatics, Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden., Chopra G; Department of Chemistry, College of Science, Purdue University, West Lafayette, IN, USA.; Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN, USA.; Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA.; Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.; Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA., Adhikari B; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA., Bhattacharya D; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.; Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA., Blake L; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Bortot LO; Laboratory of Biological Physics, Faculty of Pharmaceutical Sciences at Ribeirão Preto, University of São Paulo, São Paulo, Brazil., Cao R; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA., Dhanasekaran BK; Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India., Dimas I; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Faccioli RA; Institute of Mathematical and Computer Sciences, University of São Paulo, São Paulo, Brazil., Faraggi E; Research and Information Systems, LLC, Carmel, IN, USA.; Department of Biochemistry and Molecular Biology, IU School of Medicine, Indianapolis, IN, USA.; Batelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA., Ganzynkowicz R; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Ghosh S; Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India., Ghosh S; Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India., Giełdoń A; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Golon L; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., He Y; School of Engineering, University of California, Merced, CA, USA., Heo L; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Hou J; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA., Khan M; Department of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA., Khatib F; Department of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA., Khoury GA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA., Kieslich C; Texas A&M Energy Institute, Texas A&M University, College Station, TX, USA., Kim DE; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Krupa P; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Lee GR; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Li H; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.; School of Computer Science and Information Technology, NorthEast Normal University, Changchun, China.; Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA., Li J; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA., Lipska A; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Liwo A; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Maghrabi AHA; Biomedical Sciences Division, School of Biological Sciences, University of Reading, Reading, RG6 6AS, UK., Mirdita M; Max Planck Institute for Biophysical Chemistry, Göttingen, Germany., Mirzaei S; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; California State Polytechnic University, Pomona, CA, USA., Mozolewska MA; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Onel M; Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA., Ovchinnikov S; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Shah A; Department of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA., Shah U; Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA., Sidi T; Department of Computer Science, Ben Gurion University of the Negev, Be'er sheva, Israel., Sieradzan AK; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Ślusarz M; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Ślusarz R; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Smadbeck J; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA., Tamamis P; Texas A&M Energy Institute, Texas A&M University, College Station, TX, USA.; Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA., Trieber N; Department of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA., Wirecki T; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Yin Y; Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA., Zhang Y; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA., Bacardit J; Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing, Newcastle University, Newcastle-upon-Tyne, UK., Baranowski M; Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland., Chapman N; Center for Game Science, Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA., Cooper S; College of Computer and Information Science, Northeastern University, Boston, MA, USA., Defelicibus A; Institute of Mathematical and Computer Sciences, University of São Paulo, São Paulo, Brazil., Flatten J; Center for Game Science, Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA., Koepnick B; Department of Biochemistry, University of Washington, Seattle, WA, USA., Popović Z; Center for Game Science, Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA., Zaborowski B; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Baker D; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.; Center for Game Science, Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA., Cheng J; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA., Czaplewski C; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Delbem ACB; Institute of Mathematical and Computer Sciences, University of São Paulo, São Paulo, Brazil., Floudas C; Texas A&M Energy Institute, Texas A&M University, College Station, TX, USA., Kloczkowski A; Faculty of Chemistry, University of Gdansk, Gdańsk, Poland., Ołdziej S; Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland., Levitt M; Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA., Scheraga H; Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA., Seok C; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Söding J; Max Planck Institute for Biophysical Chemistry, Göttingen, Germany., Vishveshwara S; Molecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India., Xu D; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.; Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA., Crivelli SN; Lawrence Berkeley National Laboratory, Berkeley, CA, USA. SNCrivelli@lbl.gov.; Department of Computer Science, University of California, Davis, CA, USA. SNCrivelli@lbl.gov.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2018 Jul 02; Vol. 8 (1), pp. 9939. Date of Electronic Publication: 2018 Jul 02.
DOI: 10.1038/s41598-018-26812-8
Abstrakt: 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.
Databáze: MEDLINE