Publications

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Santini S, Derreumaux P.  2004.  Helix H1 of the prion protein is rather stable against environmental perturbations: molecular dynamics of mutation and deletion variants of PrP(90-231). Cell. Mol. Life Sci.. 61:951–960.
Bocahut A., Derrien V., Bernad S., Sebban P., Sacquin-Mora S, Guittet E., Lescop E..  2013.  Heme orientation modulates histidine dissociation and ligand binding kinetics in the hexacoordinated human neuroglobin. J. Biol. Inorg. Chem.. 18:111–122.
Ziolkowska K, Derreumaux P, Folichon M, Pellegrini O, Regnier P, , Hajnsdorf E.  2006.  Hfq variant with altered RNA binding functions. Nucleic Acids Res.. 34:709–720.
Lagarde N, Carbone A, Sacquin-Mora S.  2018.  Hidden partners: Using cross‐docking calculations to predict binding sites for proteins with multiple interactions. Proteins: Structure, Function, and Bioinformatics. 00:1-15.
Robert CH.  1990.  A hierarchical `nesting' approach to describe the stability of alpha helices with side-chain interactions. Biopolymers. 30:335–347.
Mazur AK.  1998.  Hierarchy of fast motions in protein dynamics. J. Phys. Chem. B. 102:473–479.
Man VHoang, Nguyen PH, Derreumaux P.  2017.  High-Resolution Structures of the Amyloid-β 1-42 Dimers from the Comparison of Four Atomistic Force Fields.. J Phys Chem B. 121(24):5977-5987.
Pasquali S, Derreumaux P.  2010.  HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA. J. Phys. Chem. B. 114:11957–11966.
Mazur AK.  2016.  Homologous Pairing between Long DNA Double Helices. Phys. Rev. Lett.. 116:158101.
Hegger R, Altis A, Nguyen PH, Stock G.  2007.  How complex is the dynamics of peptide folding? Phys. Rev. Lett.. 98
Kalimeri M, Rahaman O, Melchionna S, Sterpone F.  2013.  How Conformational Flexibility Stabilizes the Hyperthermophilic Elongation Factor G-Domain. J. Phys. Chem. B. 117:13775–13785.
Costa MGS, Batista PR, Shida CS, Robert CH, Bisch PM, Pascutti PG.  2010.  How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics. Bmc Genomics. 11, S5
Stirnemann G, Kang S-gu, Zhou R, Berne BJ.  2014.  How force unfolding differs from chemical denaturation.. Proc. Natl. Acad. Sci. U.s.a. 111:3413–8.
Mondal J, Halverson D, Li ITS, Stirnemann G, Walker GC, Berne BJ.  2015.  How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory.. Proc. Natl. Acad. Sci. Usa. 112:9270–5.
Pizzitutti F, Marchi M, Sterpone F, Rossky PJ.  2007.  How protein surfaces induce anomalous dynamics of hydration water. J. Phys. Chem. B. 111:7584–90.
Spichty M, Taly A, Hagn F, Kessler H, Barluenga S, Winssinger N, Karplus M.  2009.  The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15 N chemical shifts. Biophys. Chem.. 143:111–123.
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.
Roth CA, Dreyfus T, Robert CH, Cazals F.  2016.  Hybridizing Rapidly Exploring Random Trees and Basin Hopping Yields an Improved Exploration of Energy Landscapes. J. Comput. Chem.. 37:752.
Briganti G, D'arrigo G, Maccarini M, Pierleoni C, Sterpone F.  2005.  Hydration and thermodynamic equilibrium of non-ionic surfactant in solution. Coll Surf A. 261:93–99.
Chiricotto M, Melchionna S, Derreumaux P, Sterpone F.  2016.  Hydrodynamic Effects on Amyloid-beta Aggregation. Biophys. J.. 110:219A.
Chiricotto M, Melchionna S, Derreumaux P, Sterpone F.  2016.  Hydrodynamic effects on beta-amyloid (16-22) peptide aggregation. J. Chem. Phys.. 145
Hénin J., Chipot C.  2006.  Hydrogen-bonding patterns of cholesterol in lipid membranes. Chem. Phys. Lett.. 425:329–335.

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