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Leprivier G., Baillat D., Begue A., Hartmann B., Aumercier M..  2009.  Ets-1 p51 and p42 isoforms differentially modulate Stromelysin-1 promoter according to induced DNA bend orientation. Nucleic Acids Res.. 37:4341–4352.
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.
Sterpone F, Bonella S, Meloni S.  2012.  Early Stage of the Dehydrogenation of NaAlH4 by Ab Initio Rare Event Simulations. The Journal of Physical Chemistry C. 116:19636–19643.
Derreumaux P, Wei GH, Santini S, Mousseau NN.  2004.  Early steps of amyloid-petide oligomerisation explored by simulations. Neurobiol. Aging. 25:S143.
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.
Laage D, Stirnemann G.  2019.  Effect of Ions on Water Dynamics in Dilute and Concentrated Aqueous Salt Solutions. J Phys Chem B. 123:3312-3324.
Rahaman O., Melchionna S., Laage D., Sterpone F..  2013.  The effect of protein composition on hydration dynamics. Phys. Chem. Chem. Phys.. 15:3570–3576.
Viet MHoang, Nguyen PHoang, Derreumaux P, Li MSuan.  2014.  Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of A beta 40 and A beta 42. Acs Chem. Neurosci.. 5:646–657.
Viet MHoang, Nguyen PHoang, Ngo STung, Li MSuan, Derreumaux P.  2013.  Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of A beta(40) and A beta(42). Acs Chem. Neurosci.. 4:1446–1457.
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.
Nguyen PHoang, Li MSuan, Derreumaux P.  2011.  Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer. Phys. Chem. Chem. Phys.. 13:9778–9788.
Man VHoang, He X, Derreumaux P, Ji B, Xie X-Q, Nguyen PHoang, Wang J.  2019.  Effects of all-atom molecular mechanics force fields on amyloid peptide assembly: the case of aβ16–22 dimer. Journal of chemical theory and computation. 15:1440–1452.
Lu Y, Wei G, Derreumaux P.  2011.  Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-beta Fragment 29-42 by Replica Exchange Molecular Dynamics Simulations. J. Phys. Chem. B. 115:1282–1288.
Li H, Luo Y, Derreumaux P, Wei G.  2010.  Effects of the RGTFEGKF Inhibitor on the Structures of the Transmembrane Fragment 70-86 of Glycophorin A: An All-Atom Molecular Dynamics Study. J. Phys. Chem. B. 114:1004–1009.
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.
Phuong NH, Germano G, Schmid F.  2001.  Elastic constants from direct correlation functions in nematic liquid crystals: A computer simulation study. J. Chem. Phys.. 115:7227–7234.
Valle-Orero J, Eckels E, Stirnemann G, Popa I, Berkovich R, Fernandez JM.  2015.  The elastic free energy of a tandem modular protein under force.. Biochem. Biophys. Res. Comm.. :1–5.
Stirnemann G, Giganti D, Fernandez JM, Berne BJ.  2013.  Elasticity, structure, and relaxation of extended proteins under force.. Proc. Natl. Acad. Sci. U.s.a. 110:3847–52.
Mazur AK.  2008.  The electrostatic origin of low-hydration polymorphism in DNA. Chemphyschem in Press. 9:2691–2694.
Mazur AK.  2005.  Electrostatic polymer condensation and the A/B polymorphism in DNA: Sequence effects. J. Chem. Theory Comput.. 1:325–336.
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.
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.
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.
Nguyen PHoang, Derreumaux P, Stock G.  2009.  Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study. J. Phys. Chem. B. 113:9340–9347.
Mu YG, Nguyen PHoang, Stock G.  2005.  Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins: Struct., Funct., Bioinf.. 58:45–52.

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