Publications

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2008
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.
2009
Mazur AK.  2009.  Analysis of accordion DNA stretching revealed by the gold cluster ruler. Phys. Rev. E. 80:010901.
Francia F., Malferrari M., Sacquin-Mora S, Venturoli G..  2009.  Charge Recombination Kinetics and Protein Dynamics in Wild Type and Carotenoid-less Bacterial Reaction Centers: Studies in Trehalose Glasses. J. Phys. Chem. B. 113:10389–1398.
Drevelle A, Urvoas A, Ben Hamida-Rebai M, Van Vooren G, Nicaise M, Valerio-Lepiniec M, Desmadril M, Robert CH, Minard P.  2009.  Disulfide bond substitution by directed evolution in an engineered binding-protein scaffold.. Chembiochem. 10:1349–1359.
Maupetit J, Derreumaux P, Tuffery P.  2009.  A fast method for large-scale De Novo peptide and miniprotein structure prediction.. J. Comput. Chem..
Sterpone F, Bertonati C, Briganti G, Melchionna S.  2009.  Key role of proximal water in regulating thermostable proteins. J. Phys. Chem. B. 113:131–7.
Mazur AK.  2009.  Kinetic and thermodynamic DNA elasticity at micro- and mesoscopic scales. J. Phys. Chem. B. 113:2077–2089.
Mazur AK.  2009.  Modeling DNA dynamics under steady deforming forces and torques. J. Chem. Theory Comput.. 5:2149–2157.
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.
Deliot N, Chavent M, Nourry C, Lecine P, Arnaud C, Hermant A, Maigret B, Borg J.-P..  2009.  New Insight into the interaction between erbin and smad3: a non-classical binding interface for the erbin PDZ domain. Biochem. Biophys. Res. Commun.. 378:360–365.
Pasquali S., Maggs A.C..  2009.  Numerical studies of Lifshitz interactions between dielectrics. Phys. Rev. A. 79:020102(R).

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