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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.
Nguyen PH, 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.
Nguyen PH.  2009.  Estimating configurational entropy of complex molecules: A novel variable transformation approach. Chem. Phys. Lett.. 468:90–93.
Riccardi L, Nguyen PH, Stock G.  2009.  Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis. J. Phys. Chem. B. 113:16660–16668.
Park S-M, Nguyen PH, Stock G.  2009.  Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent. J. Chem. Phys.. 131
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.
Nguyen P.H., Hamm P., Stock G..  2009.  Nonequilibrium molecular dynamics simulation of photoinduced energy flow in peptides: theory meets experiment.
Bocquet N., Nury H., Baaden M, Le Poupon C., Changeux J.P, Delarue M., Corringer P.J.  2009.  X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation. Nature. 457:111–114.
Altis A, Otten M, Nguyen PH, Hegger R, Stock G.  2008.  Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis. J. Chem. Phys.. 128
Backus EHG, Nguyen PH, 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.
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.
Kobus M, Gorbunov RD, Nguyen PH, Stock G.  2008.  Nonadiabatic vibrational dynamics and spectroscopy of peptides: A quantum-classical description. Chem. Phys.. 347:208–217.
Pasquali S., Nitti F., Maggs A.C..  2008.  Numerical methods for fluctuation driven interactions between dielectrics. Phys. Rev. E. 77:016705.
Colas C., Nguyen P.H., Gelly J-C., Derreumaux P..  2008.  OPERA: An OPtimized coarsed-grained Energy model for RnA. Publication Series of the John von Neumann Institute for Computing NIC Series. 40:185–187.
Backus EHG, Nguyen PH, 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.