Hünenberger, Philippe - Eidgenössische Technische Hochschule Zürich - Department of Chemistry and Applied Biosciences

研究领域

Computer Simulation of Molecular Systems

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Hünenberger, P.H., Allemann, S. & Vogel,P. Total asymmertic synthesis of 3-amino-3-deoxy-L-talose and derivatives. Carbohydr. Res., 257, 175-187 (1994). Hünenberger, P.H., Mark, A.E. & van Gunsteren, W.F. Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study. Proteins: Struct., Funct., Genet., 21, 196-213 (1995). van Gunsteren, W.F., Hünenberger, P.H., Kovacs, H., Mark, A.E. & Schiffer, C. Investigation of protein unfolding and stability by computer simulation. Phil. Trans. R. Soc. Lond. B., 348, 49-59 (1995). Hünenberger, P.H., Mark, A.E. & van Gunsteren, W.F. Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. J. Mol. Biol, 252, 492-503 (1995). van Gunsteren, W.F., Hünenberger, Mark, A.E., Smith, P.E. & Tironi, I.G. Computer simulation of protein motion. Comput. Phys. Commun., 91, 305-319 (1995). Daura, X., Hünenberger, P.H., Mark, A.E. Querol, E., Avilés, F.X. & van Gunsteren, W.F. Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment, and importance of adequate treatment of electrostatic and internal interaction. J. Am. Chem. Soc., 118, 6285-6294 (1996). van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P.K., Mark, A.E., Scott, W.R.P. & Tironi, I.G. Biomolecular simulation: The GROMOS96 manual and user guide. Verlag der Fachvereine, Zürich, pp 1-1024 (1996). Hünenberger, P.H., Granwehr, J.K., Aebischer, J.-N., Ghoneim, N., Haselbach, E. & van Gunsteren, W.F. Experimental and theoretical approach to hydrogen-bonded diastereomeric interactions in a model complex. J. Am. Chem. Soc., 119, 7533-7544 (1997). Hünenberger, P.H. & van Gunsteren, W.F. Empirical classical interaction functions for molecular simulations. In "Computer simulation of biomolecular systems, theoretical and experimental applications", Vol. III, van Gunsteren, W.F., Weiner, P.K. & Wilkinson, A.J., Eds., Kluwer/Escom Science Publishers, Dordrecht, The Netherlands, pp 3-82 (1997). Hünenberger, P.H. & van Gunsteren, W.F. Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: Influence on the simulated energetic, structural and dielectric properties of liquid water. J. Chem. Phys., 108, 6117-6134 (1998). Hünenberger, P.H. & van Gunsteren, W.F. Empirical classical force fields for molecular systems. In "Lecture Notes in Chemistry", Vol 71, Sax, A.F., Ed., Springer Verlag, Berlin, Germany, pp 177-214 (1999). Hünenberger, P.H., Helms, V., Narayana, N., Taylor, S.S. & McCammon, J.A. Determinants of ligand binding to c-AMP dependent protein kinase. Biochemistry, 38, 2358-2366 (1999). de Bakker, P.I.W., Hünenberger, P.H. & McCammon, J.A. Molecular dynamics simulations of the hyperthermophilic protein Sac7d from Sulfolobus acidocaldaricus: Contribution of salt bridges to thermostability. J. Mol. Biol., 285, 1811-1830 (1999). Hünenberger, P.H. & McCammon, J.A. Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: A continuum electrostatics study. J. Chem. Phys., 110, 1856-1872 (1999). Hünenberger, P.H. & McCammon, J.A. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatics study. Biophys. Chem., 78, 69-88 (1999). Scott, W.R.P., Hünenberger, P.H., Tironi, I.G., Mark, A.E., Billeter, S.R., Fennen, J., Torda, A.E., Huber, T., Krüger, P. & van Gunsteren, W.F. The GROMOS biomolecular simulation program package. J. Phys. Chem. A, 103, 3596-3607 (1999). Baker, N.A., Hünenberger, P.H. & McCammon, J.A. Polarization around an ion in a dielectric continuum with truncated electrostatic interactions. J. Chem. Phys., 110, 10679-10692 (1999); Erratum: J. Chem. Phys., 113, 2510-2511 (2000) Hünenberger, P.H. Lattice-sum methods for computing electrostatic interactions in molecular simulations. In "Simulation and theory of electrostatic interactions in solution : Computational chemistry, biophysics, and aqueous solutions", Pratt, L.R. & Hummer, G., Eds., American Institute of Physics, New York, U.S.A., pp 17-83 (1999). Weber, W., Hünenberger, P.H. & McCammon, J.A. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation. J. Phys. Chem. B, 104, 3668-3675 (2000). Hünenberger, P.H. Optimal charge-shaping functions for the particle-particle--particle-mesh (P3M) method for computing electrostatic interactions in molecular simulations. J. Chem. Phys., 113, 10464-10476 (2000).