Publications

Alberts B, Johnson A, Lewis J, Raff M, et al. (2002). Molecular Biology of the Cell. Garland Science, New York.   Allison SL, Schalich J, Stiasny K, Mandl CW, et al. (2001). Mutational evidence for an internal fusion peptide in flavivirus envelope protein E. J. Virol. 75: 4268-4275. http://dx.doi.org/10.1128/JVI.75.9.4268-4275.2001 PMid:11287576 PMCid:114172   Becker Y (1982). Molecular Virology: Molecular and Medical Aspects of Disease-Causing Viruses of Man and Animals. Martinus Nijhoff Publishers, Hingham.   Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, et al. (1984). Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81: 3684-3690. http://dx.doi.org/10.1063/1.448118   Berman HM, Westbrook J, Feng Z, Gilliland G, et al. (2000). The Protein Data Bank. Nucleic Acids Res. 28: 235-242. http://dx.doi.org/10.1093/nar/28.1.235 PMid:10592235 PMCid:102472   Chen VB, Arendall WB, III, Headd JJ, Keedy DA, et al. (2010). MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66: 12-21. http://dx.doi.org/10.1107/S0907444909042073 PMid:20057044 PMCid:2803126   Chen Y, Maguire T, Hileman RE, Fromm JR, et al. (1997). Dengue virus infectivity depends on envelope protein binding to target cell heparan sulfate. Nat. Med. 3: 866-871. http://dx.doi.org/10.1038/nm0897-866 PMid:9256277   Degrève L, Fuzo CA, Silva GM and Caliri A (2011a). The Stability of Extended Secondary Protein Structures: The Dengue Virus E Protein Case. In: Ninth Triennial Congress of the World Association of Theoretical and Computational Chemists Santiago de Compostela, PII-083.   Degrève L, Fuzo CA and Caliri A (2011b). Molecular simulation of the e protein from dengue virus type 2. 36th FEBS Congress of the Biochemistry for Tomorrows Medicine. FEBS J. 278: 368-368.   DVI (2012). Dengue Vaccine Initiative. Available at [http://www.denguevaccines.org/why-a-vaccine]. Accessed February 6, 2012.   Essman U, Perera L, Berkowitz ML, Darden T, et al. (1995). A smooth particle mesh Ewald method. J. Chem. Phys. 103: 8577-8592. http://dx.doi.org/10.1063/1.470117   Flint SJ, Enquist LW, Racaniello VRT and Skalka AM (2004). Principles of Virology: Molecular Biology, Pathogenesis, and Control of Animal Viruses. ASM Press, Washington.   Germi R, Crance JM, Garin D, Guimet J, et al. (2002). Heparan sulfate-mediated binding of infectious dengue virus type 2 and yellow fever virus. Virology 292: 162-168. http://dx.doi.org/10.1006/viro.2001.1232 PMid:11878919   Hess B, Bekker H, Berendsen HJC and Fraaije JGEM (1997). LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 18: 1463-1472. http://dx.doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H   Hess B, Kutzner C, van der Spoel D and Lindahl E (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4: 435-447. http://dx.doi.org/10.1021/ct700301q   Kabsch W and Sander C (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637. http://dx.doi.org/10.1002/bip.360221211 PMid:6667333   Kuhn RJ, Zhang W, Rossmann MG, Pletnev SV, et al. (2002). Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell 108: 717-725. http://dx.doi.org/10.1016/S0092-8674(02)00660-8   Leah AR (2001). Molecular Modeling: Principles and Applications. Prentice Hall, New York.   Li Z, Khaliq M, Zhou Z, Post CB, et al. (2008). Design, synthesis, and biological evaluation of antiviral agents targeting flavivirus envelope proteins. J. Med. Chem. 51: 4660-4671. http://dx.doi.org/10.1021/jm800412d PMid:18610998 PMCid:2562352   Miyamoto S and Kollman PA (1992). SETTLE - an analytical version of the shake and rattle algorithm for rigid water models. J. Comput. Chem. 13: 952-962. http://dx.doi.org/10.1002/jcc.540130805   Modis Y, Ogata S, Clements D and Harrison SC (2003). A ligand-binding pocket in the dengue virus envelope glycoprotein. Proc. Natl. Acad. Sci. U. S. A. 100: 6986-6991. http://dx.doi.org/10.1073/pnas.0832193100 PMid:12759475 PMCid:165817   Modis Y, Ogata S, Clements D and Harrison SC (2004). Structure of the dengue virus envelope protein after membrane fusion. Nature 427: 313-319. http://dx.doi.org/10.1038/nature02165 PMid:14737159   Modis Y, Ogata S, Clements D and Harrison SC (2005). Variable surface epitopes in the crystal structure of dengue virus type 3 envelope glycoprotein. J. Virol. 79: 1223-1231. http://dx.doi.org/10.1128/JVI.79.2.1223-1231.2005 PMid:15613349 PMCid:538574   Navarro-Sanchez E, Altmeyer R, Amara A, Schwarts O, et al. (2003). Dendritic-cell-specific ICAM3-grabbing non-integrin is essential for the productive infection of human dendritic cells by mosquito-cell-derived dengue viruses. EMBO Rep. 4: 723-728. http://dx.doi.org/10.1038/sj.embor.embor866 PMid:12783086 PMCid:1326316   PDB (2012). Protein Data Bank. Available at [http://www.pdb.org]. Accessed February 6, 2012.   Perera R, Khaliq M and Kuhn RJ (2008). Closing the door on flaviviruses: entry as a target for antiviral drug design. Antiviral Res. 80: 11-22. http://dx.doi.org/10.1016/j.antiviral.2008.05.004 PMid:18585795 PMCid:2646114   Pokidysheva E, Zhang Y, Battisti AJ, Bator-Kelly CM, et al. (2006). Cryo-EM reconstruction of dengue virus in complex with the carbohydrate recognition domain of DC-SIGN. Cell 124: 485-493. http://dx.doi.org/10.1016/j.cell.2005.11.042 PMid:16469696   PyMol (2012). The PyMOL Molecular Graphics System. Available at [http://sourceforge.net/projects/pymol/files/Legacy/]. Accessed February 6, 2012.   Stauffer F, Melo MN, Carneiro FA, Sousa FJ, et al. (2008). Interaction between dengue virus fusion peptide and lipid bilayers depends on peptide clustering. Mol. Membr. Biol. 25: 128-138. http://dx.doi.org/10.1080/09687680701633091 PMid:18307100   Stiasny K and Heinz FX (2006). Flavivirus membrane fusion. J. Gen. Virol. 87: 2755-2766. http://dx.doi.org/10.1099/vir.0.82210-0 PMid:16963734   van der Schaar HM, Rust MJ, Waarts BL, Ende-Metselaar H, et al. (2007). Characterization of the early events in dengue virus cell entry by biochemical assays and single-virus tracking. J. Virol. 81: 12019-12028. http://dx.doi.org/10.1128/JVI.00300-07 PMid:17728239 PMCid:2168764   van der Spoel D, Lindahl E, Hess B, van Buuren AR, et al. (2010). Gromacs User Manual Version 4.5.4. Available at [http://www.gromacs.org]. Accessed February 6, 2012.   van Gunsteren WF, Krüger P, Billeter SR, Mark AE, et al. (1996). Biomolecular Simulation: The Gromos 96 Manual and User Guide. Hoehchulverlag an du ETH, Zürich.   Volk DE, Lee YC, Li X, Thiviyanathan V, et al. (2007). Solution structure of the envelope protein domain III of dengue-4 virus. Virology 364: 147-154. http://dx.doi.org/10.1016/j.virol.2007.02.023 PMid:17395234 PMCid:1950219   WHO (2012). World Health Organization. Available at [http://www.who.int/topics/dengue/en/]. Accessed February 6, 2012.   Zhang J, Wang J, Gao N, Chen Z, et al. (2007). Up-regulated expression of β3 integrin induced by dengue virus serotype 2 infection associated with virus entry into human dermal microvascular endothelial cells. Biochem. Biophys. Res. Commun. 356: 763-768. http://dx.doi.org/10.1016/j.bbrc.2007.03.051 PMid:17382900   Zhang Y, Zhang W, Ogata S, Clements D, et al. (2004). Conformational changes of the flavivirus E glycoprotein. Structure 12: 1607-1618. http://dx.doi.org/10.1016/j.str.2004.06.019 PMid:15341726