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Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th critical assessment of techniques for protein structure prediction experiment CASP10

Kryshtafovych, A and Moult, J and Bales, P and Bazan, JF and Biasini, M and Burgin, A and Chen, C and Cochran, FV and Craig, TK and Das, R and Fass, D and Garcia-Doval, C and Herzberg, O and Lorimer, D and Luecke, H and Ma, X and Nelson, DC and van Raaij, MJ and Rohwer, F and Segall, A and Seguritan, V and Zeth, K and Schwede, T (2014) Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th critical assessment of techniques for protein structure prediction experiment CASP10. Proteins: Structure, Function and Bioinformatics. pp. 26-42.

Abstract

For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, more than 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this article, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict transmembrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin (IL)-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fiber protein gene product 17 from bacteriophage T7; the bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally, an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins. 2013 The Authors. Wiley Periodicals, Inc

Item Type: Article
Additional Information: NIBR author: Ma, X institute: NIBR- address only contributor address: (Kryshtafovych) Genome Center, University of California, Davis, CA 95616, United States (Moult) Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, United States (Moult, Bales, Chen, Herzberg, Nelson) Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, United States (Bazan, Ma) Department of Protein Engineering, Genentech, South San Francisco, CA 94080, United States (Bazan, Ma) Department of Structural Biology, Genentech, South San Francisco, CA 94080, United States (Biasini, Schwede) Biozentrum, University of Basel, Basel, 4056, Switzerland (Biasini, Schwede) SIB Swiss Institute of Bioinformatics, Basel, 4056, Switzerland (Burgin) Broad Institute, Cambridge, MA 02142, United States (Cochran, Das) Department of Biochemistry, Stanford University, Stanford, CA 94305, United States (Craig, Lorimer) Emerald Bio, Bainbridge Isle, WA 98110, United States (Das) Department of Physics, Stanford University, Stanford, CA 94305, United States (Fass) Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel (Garcia-Doval, van Raaij) Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, E-28049, Spain (Herzberg) Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States (Luecke) Department of Biochemistry and Biophysics, Center for Biomembrane Systems, University of California, Irvine, CA 92697-3900, United States (Luecke) Department of Computer Science, Center for Biomembrane Systems, University of California, Irvine, CA 92697-3900, United States (Nelson) Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, United States (Rohwer, Segall, Seguritan) Department of Biology, San Diego State University, San Diego, CA 92182, United States (Luecke, Zeth) Unidad de Biofisica (CSIC-UPV/EHU), Bizkaia, Spain (Luecke, Zeth) IKERBASQUE, Basque Foundation for Science, Bilbao, Spain (Bazan) 44th and Aspen Life Sciences, 924 4th St. N., Stillwater, MN 55082, United States (Ma) Novartis Institutes for Biomedical Research, 4560 Horton St., Emeryville, CA 94608, United States
Date Deposited: 13 Oct 2015 13:12
Last Modified: 13 Oct 2015 13:12
URI: https://oak.novartis.com/id/eprint/22668

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