Publications

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Trellet M, Ferey N, Flotyński J, Baaden M, Bourdot P.  2018.  Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data.. J Integr Bioinform. 15(2)
Baaden M, Berny F., Muzet N., Schurhammer R., Wipff G..  2000.  Separation of radioactive cations by liquid-liquid extraction: computer simulations of water / oil solutions of salts and ionophores. Proceedings of the Euradwaste 1999 conference. :390–393.
Kozin S.A, Bertho G., Mazur AK, Rabesona H., Girault J.P, Haertle T., Takahashi M., Debey P., Hoa G.H.  2001.  Sheep prion protein synthetic peptide spanning helix 1 and beta-strand 2 (residues 142-166) shows beta-hairpin structure in solution. J. Biol. Chem.. 276:46364–46370.
Guharoy M, Janin J\�el, Robert CH.  2010.  Side-chain rotamer transitions at protein-protein interfaces. Proteins: Struct., Funct., Bioinf.. 78:3219–25.
Robert CH, Ho PS.  1995.  Significance of bound water to local chain conformations in protein crystals. Proc. Natl. Acad. Sci. U.s.a.. 92:7600–7604.
Derreumaux P.  2008.  Simulating the early steps of amyloid fibril formation and disassembly. Publication Series of the John von Neumann Institute for Computing NIC Series. 40:7–12.
Cote S, Laghaei R, Derreumaux P, Mousseau N.  2011.  Simulation of the Oligomerization Pathway for Different Alloforms of the Amyloid Beta Protein Related to Alzheimer's Disease. Biophys. J.. 100:401.
Kobus M, Lieder M, Nguyen PH, Stock G.  2011.  Simulation of transient infrared spectra of a photoswitchable peptide. J. Chem. Phys.. 135
Baaden M.  2010.  Simulations numériques de systèmes biologiques complexes : dynamique, structure et fonction de transporteurs, canaux et enzymes.
Hubert P, Sawma P, Duneau J-P, Khao J, Hénin J, Bagnard D, Sturgis J.  2010.  Single-spanning transmembrane domains in cell growth and cell-cell interactions: More than meets the eye? Cell Adh. Migr.. 4:313–324.
Kamashev DE, Mazur AK.  2004.  Single-stranded breaks relax intrinsic curvature in DNA? Biochemistry. 43:8160–8168.
Lu D, Danilowicz C, Tashjian TF, Prévost C, Godoy VG, Prentiss M.  2019.  Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology. J Biol Chem. 294:8606-8616.
Lu Y, Shi X-F, Salsbury FR, Derreumaux P.  2017.  Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42).. J Chem Phys. 146(14):145101.
Lesage A., Lelièvre T., Stoltz G., Hénin J.  2017.  Smoothed biasing forces yield unbiased free energies with the extended-system Adaptive Biasing Force method. J. Phys. Chem. B. 121(15):3676–3685.
Robert CH, Janin J.  1998.  A soft, mean–field potential derived from crystal contacts for predicting protein–protein interactions. J. Mol. Biol.. 283:1037–1047.
Bornet O., Prévost C, Vovelle F., Chassignol M., Thuong N.T, Lancelot G..  1995.  Solution structure of oligonucleotides covalently linked to a psoralen derivative.. Nucleic Acids Res.. 23:788–795.
Schmid F, Phuong NH.  2002.  Spatial order in liquid crystals: Computer simulations of systems of ellipsoids. MORPHOLOGY OF CONDENSED MATTER: PHYSICS AND GEOMETRY OF SPATIALLY COMPLEX SYSTEMS. 600:172–186.
Sterpone F, Briganti G, Pierleoni C.  2009.  Sphere versus cylinder: the effect of packing on the structure of nonionic C12E6 micelles. Langmuir. 25:8960–7.
Chiche L, Heitz A, Gelly JC, Gracy J, Chau PTT, Ha PT, Hernandez JF, Le-Nguyen D.  2004.  Squash inhibitors: From structural motifs to macrocyclic knottins. Current Protein \& Peptide Science. 5:341–349.
Katava M, Kalimeri M, Stirnemann G, Sterpone F.  2016.  Stability and Function at High Temperature. What Makes a Thermophilic GTPase Different from Its Mesophilic Homologue. J. Phys. Chem. B. 120:2721–2730.
Gnutt D, Timr S, Ahlers J, König B, Manderfeld E, Heyden M, Sterpone F, Ebbinghaus S.  2019.  Stability Effect of Quinary Interactions Reversed by Single Point Mutations. Journal of the American Chemical Society. 141:4660-4669.
Ngo STung, Nguyen PHoang, Derreumaux P.  2020.  Stability of Aβ11-40 Trimers with Parallel and Antiparallel β-Sheet Organizations in a Membrane-Mimicking Environment by Replica Exchange Molecular Dynamics Simulation. The Journal of Physical Chemistry B.
Mazur AK.  2008.  Statistics of time-limited ensembles of bent DNA conformations. J. Phys. Chem. B. 112:4975–4982.
Chakraborty D, Taly A, Sterpone F.  2015.  Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins The Journal of Physical Chemistry B. 119:12760–12770.
Cole RB, Prévost C, Tabet JC.  1989.  Stereospecific Ion-Molecule reactions in the collision cell induced by nucleophilic gas phase reagents on CI/NH4+ protonated diastereoisomeric tetracyclic terpenes.. Advances in Mass Spectrometry. 11:1056.

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