Publications

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2009
Delalande O., Férey N, Grasseau G., Baaden M.  2009.  Complex molecular assemblies at hand via interactive simulations. J. Comput. Chem.. 30:2375–2387.
Taly A, Corringer P.J, Guedin D., Lestage P., Changeux J-P.  2009.  Nicotinic receptors: allosteric transitions and therapeutic targets in the nervous system. Nat. Rev. Drug Discov.. 8:733–750.
Goncalves C., Ardourel M.Y, Decoville M., Breuzard G., Midoux P., Hartmann B., Pichon C..  2009.  An optimized extended DNA kappa B site that enhances plasmid DNA nuclear import and gene expression. J. Gene Med.. 11:401–411.
Adkins NL, McBryant SJ, Johnson CN, Leidy JM, Woodcock CL, Robert CH, Hansen JC, Georgel PT.  2009.  Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers.. Biochemistry. 48:276–288.
Lu Y, Derreumaux P, Guo Z, Mousseau N, Wei G.  2009.  Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent. Proteins: Struct., Funct., Bioinf.. 75:954–963.
2008
Guerlet G., Taly A, L. de Carvalho P, Martz A., Jiang R., Specht A., Le Novere N., Grutter T..  2008.  Comparative models of P2X2 receptor support inter-subunit ATP-binding sites. Biochem. Biophys. Res. Commun.. 375:405–409.
Guerlet G., Taly A, L. de Carvalho P, Martz A., Jiang R., Specht A., Le Novere N., Grutter T..  2008.  Comparative models of P2X2 receptor support inter-subunit ATP-binding sites. Biochem. Biophys. Res. Commun.. 375:405–409.
Guerlet G, Taly A, De Carvalho LPrado, Martz A, Jiang R, Specht A, Le Novere N, Grutter T.  2008.  Comparative models of P2X2 receptor support inter-subunit ATP-binding sites. Biochem. Biophys. Res. Commun.. 375:405–409.
Guerlet G, Taly A, De Carvalho LPrado, Martz A, Jiang R, Specht A, Le Novere N, Grutter T.  2008.  Comparative models of P2X2 receptor support inter-subunit ATP-binding sites. Biochem. Biophys. Res. Commun.. 375:405–409.
Sterpone F, Spanu L, Ferraro L, Sorella S, Guidoni L.  2008.  Dissecting the Hydrogen Bond: A Quantum Monte Carlo Approach. J Chem Theo Comp. 4:1428–1434.
Férey N, Delalande O., Grasseau G., Baaden M.  2008.  From Interactive to Immersive Molecular Dynamics. Workshop on Virtual Reality Interaction and Physical Simulation (VRIPHYS 08 - Eurographics). :89–96.
Gracy J, Le-Nguyen D, Gelly J-C, Kaas Q, Heitz A, Chiche L.  2008.  KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007. Nucleic Acids Res.. 36:D314-D319.
Gracy J, Le-Nguyen D, Gelly J-C, Kaas Q, Heitz A, Chiche L.  2008.  KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007. Nucleic Acids Res.. 36:D314-D319.
Beautrait A, Leroux V, Chavent M, Ghemtio L, Devignes M.-D, Smail-Tabbone M, Cai W, Shao X, Moreau G, Bladon P et al..  2008.  Multiple-step virtual screening using VSM-G: Overview and validation of fast geometrical matching enrichment. J. Mol. Model.. 14:393–401.
Kobus M, Gorbunov RD, Nguyen PHoang, Stock G.  2008.  Nonadiabatic vibrational dynamics and spectroscopy of peptides: A quantum-classical description. Chem. Phys.. 347:208–217.
Colas C., Nguyen PHoang, Gelly J-C., Derreumaux P.  2008.  OPERA: An OPtimized coarsed-grained Energy model for RnA. Publication Series of the John von Neumann Institute for Computing NIC Series. 40:185–187.
Cox K, Bond PJ, Grottesi A, Baaden M, Sansom MSP.  2008.  Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers. European Biophysics Journal with Biophysics Letters. 37:131–141.
Férey N, Delalande O., Grasseau G., Baaden M.  2008.  A VR Framework for Interacting with Molecular Simulations. Symposium on Virtual Reality Software and Technology (ACM-VRST 2008). :91–94.
Sterpone F, Spanu L., Ferraro L., Sorella S., Guidoni L..  2008.  Water-water hydrogen bond studied by QMC. J. Chem. Theory. Comput.. 4:1428–1432.
2007
Krieger E., Leger L., Durrieu M.P., Taib N., Bond P., Laguerre M., Lavery R., Sansom M.S.P., Baaden M.  2007.  Atomistic modeling of the membrane-embedded synaptic fusion complex: a grand challenge project on the DEISA HPC infrastructure. ParCo 2007, Parallel Computing: Architectures, Algorithms and Applications. 38:729–736.
Melquiond A., Gelly J.C., Mousseau N., Derreumaux P.  2007.  Probing amyloid fibril formation of the NFGAIL peptide by computer simulations. J. Chem. Phys.. 126:065101.
Bocquet N., L. de Carvalho P, Cartaud J., Neyton J., Le Poupon C., Taly A, Grutter T., Changeux J-P, Corringer P.J.  2007.  A prokaryotic proton-gated ion channel from the nicotinic acetylcholine receptor family. Nature. 445:116–119.
Gorbunov RD, Nguyen PHoang, Kobus M, Stock G.  2007.  Quantum-classical description of the amide I vibrational spectrum of trialanine. J. Chem. Phys.. 126
Férey N, Toffano-Nioche C, Matte-Taillez O, Gherbi R, Turner W.  2007.  REVIVOS: REalité VIrtuelle pour la construction de VOcabulaires Spécialisés. Journées Francophones d'Ingénierie des Connaissances (AFIA-IC 2007).
Graf J, Nguyen PHoang, Stock G, Schwalbe H.  2007.  Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study. J. Am. Chem. Soc.. 129:1179–1189.

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