Publications

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Timsit Y, Shatzky-Schwartz M., Shakked Z..  1999.  Left-handed DNA crossovers. Implications for DNA-DNA recognition and structural alterations. J. Biomol. Struct. Dyn.. 16:775–785.
Garret M., Boue-Grabot E., Taly A.  2014.  Long distance effect on ligand-gated ion channels extracellular domain may affect interactions with the intracellular machinery. Commun. Integr. Biol.. 7:e27984.
Baaden M, Burgard M, Boehme C, Wipff G.  2001.  Lanthanide cation binding to a phosphoryl-calix[4]arene: the importance of solvent and counterions investigated by molecular dynamics and quantum mechanical simulations. Phys. Chem. Chem. Phys.. 3:1317–1325.
Tran T-T, Nguyen PH, Derreumaux P.  2016.  Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer’s peptides. J. Chem. Phys.. 144
Lemoine D, Jiang R, Taly A, Chataigneau T, Specht A, Grutter T.  2012.  Ligand-gated ion channels: new insights into neurological disorders and ligand recognition. Chem. Rev.. 112:6285–6318.
Sterpone F, Ceccarelli M., Marchi M..  2003.  Linear response and electron transfer in complex biomolecules systems and Reaction Center Protein. J. Phys. Chem. B. 107:11208–11215.
Robert CH, Fall L, Gill SJ.  1988.  Linkage of organic phosphates to oxygen binding in human hemoglobin at high concentrations. Biochemistry. 27:6835–6843.
Beaugrand M\"ıwenn, Arnold AA, Hénin J, Warschawski DE, Williamson PTF, Marcotte I.  2014.  Lipid concentration and molar ratio boundaries for the use of isotropic bicelles.. Langmuir. 30:6162–6170.
Moraga-Cid G., Sauguet L., Huon C., Malherbe L., Girard-Blanc C., Petres S., Murail S., Taly A, Baaden M, Delarue M. et al..  2015.  Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure. Proc. Natl. Acad. Sci. U.s.a.. 112:2865–2870.
Mazur AK.  2011.  Local elasticity of strained DNA studied by all-atom simulations. Phys. Rev. E. 84:021903.
Phuong NH, Schmid F.  2003.  Local structure in nematic and isotropic liquid crystals. J. Chem. Phys.. 119:1214–1222.
Sacquin-Mora S, Laforet E, Lavery R.  2007.  Locating the active sites of enzymes using mechanical properties. Proteins: Struct., Funct., Bioinf.. 67:350–359.
Derreumaux P, SCHLICK T.  1995.  LONG TIMESTEP DYNAMICS OF PEPTIDES BY THE DYNAMICS DRIVER APPROACH. Proteins-structure Function and Genetics. 21:282–302.
Derreumaux P, Schlick T..  1998.  The loop opening/closing motion of the enzyme triosephosphate isomerase. Biophys. J.. 74:72–81.
De Simone A, Derreumaux P.  2010.  Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: A replica exchange molecular dynamics study in explicit solvent. J. Chem. Phys.. 132:165103.
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Saladin A, Amourda C., Poulain P., Ferey N., Baaden M, Zacharias M., Delalande O., Prévost C.  2010.  Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res.. 38:6313–6323.
Sacquin-Mora S, Lavery R..  2009.  Modeling the Mechanical Response of Proteins to Anisotropic Deformation. Chemphyschem. 10:115–118.
Hirst J.D, Glowacki D.R, Baaden M.  2014.  Molecular simulations and visualization: introduction and overview. Faraday Discuss.. 169:9–22.
Grutter T., de Carvalho L.P, Dufresne V., Taly A, Edelstein S.J, Changeux J-P.  2005.  Molecular tuning of fast gating in pentameric ligand-gated ion channels. Proc. Natl. Acad. Sci. U.s.a.. 102:18207–18212.
Jiang R., Taly A, Grutter T..  2013.  Moving through the gate in ATP-activated P2X receptors. Trends Biochem. Sci.. 38:20–29.
Delalande O., Ferey N., Laurent B., Gueroult M., Hartmann B., Baaden M.  2010.  Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device. Pac. Symp. Biocomput.. :205–215.
Baaden M, Berny F, Madic C, Wipff G.  2000.  M3+ lanthanide cation solvation by acetonitrile: The role of cation size, counterions, and polarization effects investigated by molecular dynamics and quantum mechanical simulations. J. Phys. Chem. A. 104:7659–7671.
Sterpone F, Stirnemann G, Laage D.  2012.  Magnitude and molecular origin of water slowdown next to a protein. J. Am. Chem. Soc.. 134:4116–4119.

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