Publications

Export 782 results:
Author Title [ Type(Asc)] Year
Journal Article
Timsit Y, Moras D..  1995.  Self-fitting and self-modifying properties of the B-DNA molecule. J. Mol. Biol.. 251:629–647.
Licsandru E., Kocsis I., Shen Y.X, Murail S., Legrand Y.M, van der Lee A., Tsai D., Baaden M., Kumar M., Barboiu M..  2016.  Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation. J. Am. Chem. Soc.. 138:5403–5409.
Melquiond A, Dong X, Mousseau N, Derreumaux P.  2008.  Role of the region 23-28 in A beta fibril formation: Insights from simulations of the monomers and dimers of Alzheimer's peptides A beta 40 and A beta 42. Curr. Alzheimer Res.. 5:244–250.
Derreumaux P.  2003.  Role of supersecondary structural elements in protein G folding. J. Chem. Phys.. 119:4940–4944.
Adkins NL, McBryant SJ, Johnson CN, Leidy JM, Woodcock CL, Robert CH, Hansen JC, Georgel PT.  2009.  Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers.. Biochemistry. 48:276–288.
Rahaman O, Kalimeri M, Melchionna S, Hénin J, Sterpone F.  2015.  Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains.. J. Phys. Chem. B. 119:8939–49.
Nayeem SM, Oteri F, Baaden M, Deep S.  2017.  Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3.. J Phys Chem B. 121(22):5483-5498.
Tashjian TF, Danilowicz C, Molza A-E, Nguyen BH, Prévost C, Prentiss M, Godoy VG.  2019.  Residues in the fingers domain of the translesion DNA polymerase DinB enable its unique participation in error-prone double-strand break repair. J Biol Chem. 294:7588-7600.
Nishikawa N., Nguyen P., Derreumaux P., Okamoto Y..  2013.  Replica-exchange molecular dynamics simulations of the amyloid-beta(16-22) fragments. European Biophysics Journal with Biophysics Letters. 42:S68.
Nishikawa N, Nguyen PH, Derreumaux P, Okamoto Y.  2015.  Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation. Mol. Simul.. 41:1041–1044.
Nguyen PH.  2010.  Replica exchange simulation method using temperature and solvent viscosity. J. Chem. Phys.. 132
Chebaro Y, Dong X, Laghaei R, Derreumaux P, Mousseau N.  2009.  Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.. J. Phys. Chem. B. 113:267–274.
Vartia AA, Mitchell-Koch KR, Stirnemann G, Laage D, Thompson WH.  2011.  On the reorientation and hydrogen-bond dynamics of Alcohols. J. Phys. Chem. B. 115:12173–12178.
Laage D, Stirnemann G, Sterpone F, Rey R, Hynes JT.  2011.  Reorientation and Allied Dynamics in Water and Aqueous Solutions. Annu. Rev. Phys. Chem.. 62:395–416.
Stirnemann G, Sterpone F.  2015.  Recovering protein thermal stability using all-atom Hamiltonian replica-exchange simulations in explicit solvent. J. Chem. Theo. Comput.. 11:5573–5577.
Kim R, Kanamaru S, Mikawa T, Prévost C, Ishii K, Ito K, Uchiyama S, Oda M, Iwasaki H, Kim SK et al..  2018.  RecA requires two molecules of Mg2+ ions for its optimal strand exchange activity in vitro. Nucleic Acids Res. ahead of print
Chakravarty D, Guharoy M, Robert CH, Chakrabarti P, Janin J.  2013.  Reassessing buried surface areas in protein-protein complexes.. Protein Sci.. 22:1453–57.
Nguyen PH, Staudt H, Wachtveitl J, Stock G.  2011.  Real Time Observation of Ultrafast Peptide Conformational Dynamics: Molecular Dynamics Simulation vs Infrared Experiment. J. Phys. Chem. B. 115:13084–13092.
Man VHoang, Li MSuan, Derreumaux P, Nguyen PH.  2018.  Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study. The Journal of Chemical Physics. 148:094505.
Berkovich R., Hermans R.I, Popa I., Stirnemann G, Garcia-Manyes S., Berne B.J, Fernandez J.M.  2012.  Rate limit of protein elastic response is tether dependent. Proc. Natl. Acad. Sci. U.s.a.. 109:14416–14421.
PETICOLAS WL, WILSON KJ, Derreumaux P, VERGOTEN G.  1989.  RAMAN-SPECTROSCOPY, MOLECULAR-FORCE FIELDS, AND THE DYNAMICS OF BIOLOGICAL MOLECULES. Chemica Scripta. 29A:113–122.
Isabelle V, Prévost C, Spotheim-Maurizot M, Sabattier R, Charlier M.  1995.  Radiation-induced damages in single- and double-stranded DNA. Int. J. Radiat. Biol.. 67:169–76.
Bocahut A., Bernad S., Sebban P., Sacquin-Mora S.  2009.  Relating the Diffusion of Small Ligands in Human Neuroglobin to Its Structural and Mechanical Properties. J. Phys. Chem. B. 113:16257–16267.
Mazur AK.  1997.  Quasi-Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers. J. Comput. Chem.. 18:1354–1364.
Gorbunov RD, Nguyen PH, Kobus M, Stock G.  2007.  Quantum-classical description of the amide I vibrational spectrum of trialanine. J. Chem. Phys.. 126

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