Publications

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2008
Dong X, Chen W, Mousseau N, Derreumaux P.  2008.  Energy landscapes of the monomer and dimer of the Alzheimer's peptide A beta(1-28). J. Chem. Phys.. 128:125108.
Backus EHG, Nguyen PHoang, Botan V, Pfister R, Moretto A, Crisma M, Toniolo C, Stock G, Hamm P.  2008.  Energy transport in peptide helices: A comparison between high- and low-energy excitations. J. Phys. Chem. B. 112:9091–9099.
Mousseau N, Derreumaux P.  2008.  Exploring energy landscapes of protein folding and aggregation. Front. Biosci.. 13:4495–4516.
Pasquali S., Maggs A.C..  2008.  Fluctuation-induced interactions between dielectrics. J. Chem. Phys.. 129:014703.
Kamashev D, Balandina A, Mazur AK, Arimondo PB, Rouviere-Yan, iv J.  2008.  HU binds and folds single-stranded DNA. Nucl. Acids Res.. 36:1026–1036.
Brovchenko I, Krukau A, Oleinikova A, Mazur AK.  2008.  Ion dynamics and water percolation effects in DNA polymorphism. J. Am. Chem. Soc.. 130:121–131.
Chavent M, Levy B, Maigret B.  2008.  MetaMol: High quality visualization of Molecular Skin Surface. J. Mol. Graphics Modell.. 27:209–213.
Neri M, Baaden M, Carnevale V, Anselmi C, Maritan A, Carloni P.  2008.  Microseconds dynamics simulations of the outer-membrane protease T. Biophys. J.. 94:71–78.
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.
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.
Pasquali S., Nitti F., Maggs A.C..  2008.  Numerical methods for fluctuation driven interactions between dielectrics. Phys. Rev. E. 77:016705.
Sterpone F, Briganti G, Melchionna S, Pierleoni C.  2008.  Pressure-induced core packing and interfacial dehydration in nonionic C12E6 micelle in aqueous solution. Langmuir. 24:6067–71.
Melquiond A, Dong X, Mousseau N, Derreumaux P.  2008.  Role of the region 23-28 in A beta fibril formation: Insights from simulations of the monomers and dimers of Alzheimer's peptides A beta 40 and A beta 42. Curr. Alzheimer Res.. 5:244–250.
Melquiond A, Dong X, Mousseau N, Derreumaux P.  2008.  Role of the region 23-28 in A beta fibril formation: Insights from simulations of the monomers and dimers of Alzheimer's peptides A beta 40 and A beta 42. Curr. Alzheimer Res.. 5:244–250.
Wei G, Song W, Derreumaux P, Mousseau N.  2008.  Self-assembly of amyloid-forming peptides by molecular dynamics simulations. Front. Biosci.. 13:5681–5692.
Song W, Wei G, Mousseau N, Derreumaux P.  2008.  Self-assembly of the beta 2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals beta-barrel species. J. Phys. Chem. B. 112:4410–4418.
Mazur AK.  2008.  Statistics of time-limited ensembles of bent DNA conformations. J. Phys. Chem. B. 112:4975–4982.
Backus EHG, Nguyen PHoang, Botan V, Moretto A, Crisma M, Toniolo C, Zerbe O, Stock G, Hamm P.  2008.  Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties. J. Phys. Chem. B. 112:15487–15492.
Férey N, Bouyer G., Martin C., Bourdot P., Nelson J., Burkhardt andJM.  2008.  User Needs Analysis to Design a 3D Multimodal Protein-Docking Interface. Symposium on 3D User Interfaces 2008 (3DUI 2008 - IEEE). :125–132.
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.
Maupetit J, Tuffery P, Derreumaux P.  2007.  A coarse-grained protein force field for folding and structure prediction. Proteins: Struct., Funct., Bioinf.. 69:394–408.
Derreumaux P, Mousseau N.  2007.  Coarse-grained protein molecular dynamics simulations. J. Chem. Phys.. 126:025101.
Wei G, Mousseau N, Derreumaux P.  2007.  Computational Simulations of the Early Steps of Protein Aggregation. Prion. 1:3–8.
Atmane N, Dairou J, Flatters D, Martins M, Pluvinage B, Derreumaux P, Dupret J-M, Rodrigues-Lima F.  2007.  The conserved glycine/alanine residue of the active-site loop containing the putative acetylCoA-binding motif is essential for the overall structural integrity of Mesorhizobium loti arylamine N-acetyltransferase 1. Biochem. Biophys. Res. Commun.. 361:256–262.
Botan V, Backus EHG, Pfister R, Moretto A, Crisma M, Toniolo C, Nguyen PHoang, Stock G, Hamm P.  2007.  Energy transport in peptide helices. Proc. Natl. Acad. Sci. U.s.a.. 104:12749–12754.

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