Publications

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B
Baaden M.  2000.  Etudes de molécules extractantes en solution et aux interfaces liquide-liquide: aspects structuraux et mécanistiques des effets de synergie.
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.
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.
Brannigan G, Hénin J, Law R, Eckenhoff RG, Klein ML.  2008.  Embedded cholesterol in the nicotinic acetylcholine receptor. Proc. Natl. Acad. Sci. U.s.a.. 105:14418–14423.
C
Campbell JD, Biggin PC, Baaden M, Sansom MSP.  2003.  Extending the structure of an ABC transporter to atomic resolution: Modeling and simulation studies of MsbA. Biochemistry. 42:3666–3673.
Catoire L.J, Damian M., Baaden M, Guittet E., Banères J.-L..  2011.  Electrostatically–driven fast association and perdeuteration allow transferred cross–relaxation detection for G protein–coupled receptor ligands with equilibrium dissociation constants in the high–to–low nanomolar range. J Biomolecular Nmr. 50:191–5.
Chipot C, Hénin J.  2005.  Exploring the free energy landscape of a short peptide using an average force. J. Chem. Phys.. 123:244906.
D
da Silva FLuis Barro, Pasquali S, Derreumaux P, Dias LGustavo.  2016.  Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin. Soft Matter. 12:5600–5612.
Delalande O., Sacquin-Mora S, Baaden M.  2011.  Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase. Biophys. J.. 101:1440–1449.
Derreumaux P.  2009.  Exploring amyloid aggregates with the OPEP coarse-grained force field. Abstracts of Papers of the American Chemical Society. 238
Derreumaux P.  2001.  Evidence that the 127-164 region of prion proteins has two equi-energetic conformations with beta or alpha features. Biophys. J.. 81:1657–1665.
Derreumaux P, Wei GH, Santini S, Mousseau NN.  2004.  Early steps of amyloid-petide oligomerisation explored by simulations. Neurobiol. Aging. 25:S143.
Derreumaux P, VERGOTEN G.  1991.  EFFECT OF UREY-BRADLEY-SHIMANOUCHI FORCE-FIELD ON THE HARMONIC DYNAMICS OF PROTEINS. Proteins-structure Function and Genetics. 11:120–132.
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.
Dreher M, Prevoteau-Jonquet J, Trellet M, Piuzzi M, Baaden M, Raffin B, Férey N, Robert S, Limet S..  2014.  ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations. Faraday Discuss.. 169:119–142.
F
B Fas A, Sacquin-Mora S, Papaleo E.  2023.  Editorial: In Celebration of Women in Science: Biological Modeling and Simulation. Front Mol Biosci. 10:1175325.
Férey N, Gros P.-E., Hérisson J., Gherbi R..  2004.  Exploration by visualization of numerical and textual genomic data. Journal of Biological Physics and Chemistry. 4:102–110.
Férey N.  2006.  Exploration Immersive de Données Génomiques Textuelles et Factuelles : vers une approche par Visual Mining.
G
Gabb HA, Lavery R, Prévost C.  1995.  Efficient conformational space sampling for nucleosides using internal coordinate Monte-Carlo simulations and a modified furanose description. J. Comput. Chem.. 16:667–680.
Gan H.H, Pasquali S., Schlick andT.  2003.  Exploring The Repertoire of RNA Secondary Motifs Using Graph Theory with Implications for RNA Design. Nuc. Acids Res.. 31:2926–2943.
Gelly JC, Chiche L, Gracy J.  2005.  EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments. Bmc Bioinf.. 6
Gerencser L., Taly A, Baciou L., Maroti P., Sebban P..  2002.  Effect of binding of Cd2+ on bacterial reaction center mutants: proton-transfer uses interdependent pathways. Biochemistry. 41:9132–9138.
H
Hallen D., Wadso I., Wasserman D.J, Robert C.H, Gill S.J.  1988.  Enthalpy of dimerization of benzene in water. J. Phys. Chem.. 92:3623–3625.
Hénin J, Fiorin G, Chipot C, Klein ML.  2010.  Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. J. Chem. Theory Comput.. 6:35–47.
Hénin J, Lelièvre T, Shirts MR, Valsson O, Delemotte L.  2022.  Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]. Living Journal of Computational Molecular Science. 4:1583.

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