[1]
Graham, C.S.; Swan, T. A path to eradication of hepatitis C in low- and middle-income countries. Antiviral Res., 2015, 119, 89-96.
[2]
Gower, E.; Estes, C.; Blach, S.; Razavi-Shearer, K.; Razavi, H. Global epidemiology and genotype distribution of the hepatitis C virus infection. J. Hepatol., 2014, 61(1), S45-S57.
[3]
Sugiyama, K. [Genomic structure and function of untranslated region, structural region and non-structural region of hepatitis C virus RNA]. Nihon Rinsho, 2004, 62(Pt 1), 32-37.
[4]
Simmonds, P. The origin of hepatitis C virus. Curr. Top. Microbiol. Immunol., 2013, 369, 1-15.
[5]
Niepmann, M. Hepatitis C virus RNA translation. Curr. Top. Microbiol. Immunol., 2013, 369, 143-166.
[6]
Moradpour, D.; Penin, F. Hepatitis C virus proteins: from structure to function. Curr. Top. Microbiol. Immunol., 2013, 369, 113-142.
[7]
Montserret, R.; Saint, N.; Vanbelle, C.; Salvay, A.G.; Simorre, J.P.; Ebel, C.; Sapay, N.; Renisio, J.G.; Böckmann, A.; Steinmann, E.; Pietschmann, T.; Dubuisson, J.; Chipot, C.; Penin, F. NMR structure and ion channel activity of the p7 protein from hepatitis C virus. J. Biol. Chem., 2010, 285(41), 31446-31461.
[8]
Cheng, J.; Baldi, P. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics, 2007, 8, 113.
[9]
Wu, S.; Zhang, Y. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics, 2008, 24(7), 924-931.
[10]
Klepeis, J.L.; Wei, Y.; Hecht, M.H.; Floudas, C.A. Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study. Proteins, 2005, 58(3), 560-570.
[11]
Liwo, A.; Khalili, M.; Scheraga, H.A. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl. Acad. Sci. USA, 2005, 102(7), 2362-2367.
[12]
Pei, J.; Grishin, N.V. PROMALS: Towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics, 2007, 23(7), 802-808.
[13]
Sievers, F.; Wilm, A.; Dineen, D.; Gibson, T.J.; Karplus, K.; Li, W.; Lopez, R.; McWilliam, H.; Remmert, M.; Söding, J.; Thompson, J.D.; Higgins, D.G. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol., 2011, 7, 539.
[14]
Hall, H. BioEdit version 5.0.6; North Carolina State University, Department of Microbiology, 2001.
[15]
Katoh, K.; Kuma, K.; Toh, H.; Miyata, T. MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res., 2005, 33(2), 511-518.
[16]
Kumar, S.; Stecher, G.; Tamura, K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol., 2016, 33(7), 1870-1874.
[17]
Xue, Z.; Xu, D.; Wang, Y.; Zhang, Y. ThreaDom: Extracting protein domain boundary information from multiple threading alignments. Bioinformatics, 2013, 29(13), i247-i256.
[18]
Bru, C.; Courcelle, E.; Carrère, S.; Beausse, Y.; Dalmar, S.; Kahn, D. The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res., 2005, 33(Database issue), D212-D215.
[19]
Pollastri, G.; McLysaght, A. Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics, 2005, 21(8), 1719-1720.
[20]
McGuffin, L.J.; Bryson, K.; Jones, D.T. The PSIPRED protein structure prediction server. Bioinformatics, 2000, 16(4), 404-405.
[21]
Cheng, J.; Randall, A.Z.; Sweredoski, M.J.; Baldi, P. SCRATCH: A protein structure and structural feature
prediction server. Nucleic Acids Res, 2005, 33(Web
Server issue), W72-6..
[22]
Lin, K.; Simossis, V.A.; Taylor, W.R.; Heringa, J. A simple and fast secondary structure prediction method using hidden neural networks. Bioinformatics, 2005, 21(2), 152-159.
[23]
Combet, C.; Blanchet, C.; Geourjon, C.; Deléage, G. NPS@: Network protein sequence analysis. Trends Biochem. Sci., 2000, 25(3), 147-150.
[24]
Drozdetskiy, A.; Cole, C.; Procter, J.; Barton, G.J. JPred4: A protein secondary structure prediction server. Nucleic Acids Res., 2015, 43(W1), W389-94.
[25]
Rost, B.; Yachdav, G.; Liu, J. The PredictProtein server. Nucleic Acids Res., 2004, 32, W321-6.
[26]
Ko, J.; Park, H.; Heo, L.; Seok, C. GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Res., 2012, 40, W294-7.
[27]
Biasini, M.; Bienert, S.; Waterhouse, A.; Arnold, K.; Studer, G.; Schmidt, T.; Kiefer, F.; Gallo Cassarino, T.; Bertoni, M.; Bordoli, L.; Schwede, T. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res., 2014, 42, W252-8.
[28]
Yang, J.; Yan, R.; Roy, A.; Xu, D.; Poisson, J.; Zhang, Y. The I-TASSER Suite: protein structure and function prediction. Nat. Methods, 2015, 12(1), 7-8.
[29]
Ginalski, K.; Elofsson, A.; Fischer, D.; Rychlewski, L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics, 2003, 19(8), 1015-1018.
[30]
Wu, S.; Zhang, Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res., 2007, 35(10), 3375-3382.
[31]
Wallner, B.; Elofsson, A. Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics, 2005, 21(23), 4248-4254.
[32]
Kelley, L.A.; Mezulis, S.; Yates, C.M.; Wass, M.N.; Sternberg, M.J.E. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc., 2015, 10(6), 845-858.
[33]
Xu, D.; Zhang, Y. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins, 2012, 80(7), 1715-1735.
[34]
Xu, D.; Zhang, Y. Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys. J., 2011, 101(10), 2525-2534.
[35]
Bhattacharya, D.; Cheng, V. 3-Drefine: Consistent Protein Structure Refinement by Optimizing Hydrogen-Bonding Network and Atomic-Level Energy Minimization. Proteins, 2013, 81(1), 119-131.
[36]
Benkert, P.; Tosatto, S.C.E.; Schomburg, D. QMEAN: A comprehensive scoring function for model quality assessment. Proteins, 2008, 71(1), 261-277.
[37]
Benkert, P.; Biasini, M.; Schwede, T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 2011, 27(3), 343-350.
[38]
Berjanskii, M.; Liang, Y.; Zhou, J.; Tang, P.; Stothard, P.; Zhou, Y.; Cruz, J.; Macdonell, C.; Lin, G.; Lu, P.; Wishart, D.S. PROSESS: A protein structure evaluation suite and server. Nucleic Acids Res., 2010, 8, W633-40.
[39]
Laskowski, R.A.; MacArthur, M.W.; Moss, D.S.; Thornton, J.M. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Cryst., 1993, 26, 283-291.
[40]
Hooft, R.W.; Vriend, G.; Sander, C.; Abola, E.E. Errors in protein structures. Nature, 1996, 381(6580), 272.
[41]
Sigrist, C.J.A.; de Castro, E.; Cerutti, L.; Cuche, B.A.; Hulo, N.; Bridge, A.; Bougueleret, L.; Xenarios, I. New and continuing developments at PROSITE. Nucleic Acids Res., 2013, 41, D344-D347.
[42]
Henikoff, J.G.; Greene, E.A.; Pietrokovski, S.; Henikoff, S. Increased coverage of protein families with the blocks database servers. Nucleic Acids Res., 2000, 28(1), 228-230.
[43]
Henikoff, S.; Henikoff, J.G.; Pietrokovski, S. Blocks: A non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics, 1999, 15(6), 471-479.
[44]
Attwood, T.K.; Bongcam-Rudloff, E.; Brazas, M.E.; Corpas, M.; Gaudet, P.; Lewitter, F.; Mulder, N.; Palagi, P.M.; Schneider, M.V.; van Gelder, C.W. Correction: GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training. PLOS Comput. Biol., 2015, 11(5), e1004281.
[45]
Kahn, D.; Rezvoy, C.; Vivien, F. Parallel large scale inference of protein domain families. Proceedings of the 14th International Conference on Parallel and Distributed Systems, 2008, pp. 72-79.
[46]
Letunic, I.; Doerks, T.; Bork, P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Res., 2015, 43(Database issue), D257-D260.
[47]
Wan, J.; Kang, S.; Tang, C.; Yan, J.; Ren, Y.; Liu, J.; Gao, X.; Banerjee, A.; Ellis, L.B.M.; Li, T. Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection. Nucleic Acids Res., 2008, 36(4), e22.
[48]
Zhang, Y.; Skolnick, J. Scoring function for automated assessment of protein structure template quality. Proteins, 2004, 1; 57(4), 702-10.
[49]
Wu, S.; Zhang, Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res., 2007, 35(10), 3375-3382.
[50]
Eidhammer, I.; Jonassen, I.; Taylor, W.R. Protein bioinformatics: An algorithmic approach to sequence and structure analysis., 2005.
[51]
Wu, S.; Zhang, Y. MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins, 2008, 72(2), 547-556.
[52]
Atkinson, R.A.; Williams, R.J. Solution structure of the kringle 4 domain from human plasminogen by 1H nuclear magnetic resonance spectroscopy and distance geometry. J. Mol. Biol., 1990, 212(3), 541-552.
[53]
Linding, R.; Jensen, L.J.; Diella, F.; Bork, P.; Gibson, T.J.; Russell, R.B. Protein disorder prediction: implications for structural proteomics. Structure, 2003, 11(11), 1453-1459.
[54]
Laity, J.H.; Lee, B.M.; Wright, P.E. Zinc finger proteins: new insights into structural and functional diversity. Curr. Opin. Struct. Biol., 2001, 11(1), 39-46.
[55]
Madan, V.; Bartenschlager, R. Structural and Functional Properties of the Hepatitis C Virus p7 Viroporin. Viruses, 2015, 7(8), 4461-4481.
[56]
Gonzalez, M.E.; Carrasco, L. Viroporins. FEBS Lett., 2003, 552(1), 28-34.
[57]
Nieva, J.L.; Madan, V.; Carrasco, L. Viroporins: structure and biological functions. Nat. Rev. Microbiol., 2012, 10(8), 563-574.
[58]
Farazi, T.A.; Waksman, G.; Gordon, J.I. The biology and enzymology of protein N-myristoylation. J. Biol. Chem., 2001, 276(43), 39501-39504.
[59]
Hayashi, N. U.; Titani, K. N-myristoylated proteins, key components in intracellular signal transduction systems enabling rapid and flexible cell responses. Proc. J. pn. Acad., 2010, Ser. B 86, 494-508.
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