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2000 Journal Article The effect of force-field parameters on properties of liquids: Parameterization of a simple three site model for methanolWalser, Regula, Mark, Alan E., van Gunsteren, Wilfred F., Lauterbach, Monika and Wipff, Georges (2000). The effect of force-field parameters on properties of liquids: Parameterization of a simple three site model for methanol. Journal of Chemical Physics, 112 (23), 10450-10459. doi: 10.1063/1.481680 |
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2000 Journal Article On the temperature and pressure dependence of a range of properties of a type of water model commonly used in high-temperence protein unfolding simulationsWalser, Regula, Mark, Alan E. and van Gunsteren, Wilfred F. (2000). On the temperature and pressure dependence of a range of properties of a type of water model commonly used in high-temperence protein unfolding simulations. Biophysical Journal, 78 (6), 2752-2760. doi: 10.1016/S0006-3495(00)76820-2 |
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2000 Journal Article The GROMOS96 benchmarks for molecular simulationBonvin, Alexandre M. J. J., Mark, Alan E. and van Gunsteren, Wilfred F. (2000). The GROMOS96 benchmarks for molecular simulation. Computer Physics Communications, 128 (3), 550-557. doi: 10.1016/S0010-4655(99)00540-8 |
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1999 Journal Article Peptide folding simulations: No solvent required?Daura, X., van Gunsteren, W. F. and Mark, A. E. (1999). Peptide folding simulations: No solvent required?. Computer Physics Communications, 123 (1-3), 97-102. doi: 10.1016/S0010-4655(99)00261-1 |
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1999 Journal Article Estimating relative free energies from a single ensemble: Hydration free energiesSchäfer, Heiko, Van Gunsteren, Wilfred F. and Mark, Alan E. (1999). Estimating relative free energies from a single ensemble: Hydration free energies. Journal of Computational Chemistry, 20 (15), 1604-1617. doi: 10.1002/(SICI)1096-987X(19991130)20:153.0.CO;2-A |
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1999 Journal Article The effect of motional averaging on the calculation of NMR-derived structural propertiesDaura, Xavier, Antes, Iris, van Gunsteren, Wilfred F, Thiel, Walter and Mark, Alan E. (1999). The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins: Structure, Function, and Bioinformatics, 36 (4), 542-555. doi: 10.1002/(SICI)1097-0134(19990901)36:43.0.CO;2-M |
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1999 Journal Article The GROMOS biomolecular simulation program packageScott, Walter R. P., Hunenberger, Philippe H., Tironi, Ilario G., Mark, Alan E., Billeter, Salomon R., Fennen, Jens, Torda, Andrew E., Huber, Thomas, Kruger, Peter and van Gunsteren, Wilfred F. (1999). The GROMOS biomolecular simulation program package. Journal of Physical Chemistry A, 103 (19), 3596-3607. doi: 10.1021/jp984217f |
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1999 Journal Article On the validity of Stokes’ law at the molecular levelWalser, Regula, Mark, Alan E. and van Gunsteren, Wilfred F. (1999). On the validity of Stokes’ law at the molecular level. Chemical Physics Letters, 303 (5-6), 583-586. doi: 10.1016/S0009-2614(99)00266-3 |
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1999 Journal Article Folding-unfolding thermodynamics of a beta-heptapeptide form equilibrium simulationsDaura, X., van Gunsteren, W. F. and Mark, A. E. (1999). Folding-unfolding thermodynamics of a beta-heptapeptide form equilibrium simulations. Proteins: Structure, Function, and Genetics, 34 (3), 269-280. doi: 10.1002/(SICI)1097-0134(19990215)34:3 |
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1999 Journal Article Peptide Folding: When simulation meets experimentDaura, Xavier, Gadermann, Karl, Jaun, Bernhard, Seebach, Dieter, van Gunsteren, Wilfred F. and Mark, Alan E. (1999). Peptide Folding: When simulation meets experiment. Angewandte Chemie, 38 (1-2), 236-240. doi: 10.1002/(SICI)1521-3773(19990115)38:1/23.0.CO;2-M |
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1998 Journal Article On using time-averaging restraints in molecular dynamics simulationScott, Walter R. P., Mark, Alan E. and van Gunsteren, W.F. (1998). On using time-averaging restraints in molecular dynamics simulation. Journal of Biomolecular NMR, 12 (4), 501-508. doi: 10.1023/A:1008306732538 |
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1998 Journal Article Reversible peptide folding in solution by molecular dynamics simulationDaura, Xavier, Jaun, Bernhard, Seebach, Dieter, van Gunsteren, Wilfred F. and Mark, Alan E. (1998). Reversible peptide folding in solution by molecular dynamics simulation. Journal of Molecular Biology, 280 (5), 925-932. doi: 10.1006/jmbi.1998.1885 |
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1998 Journal Article Molecular dynamics simulations of peptide fragments from hen lysozyme: Insight into non-native protein conformationsSmith, Lorna J., Mark, Alan E., Dobson, Christopher M. and van Gunsteren, Wilfred (1998). Molecular dynamics simulations of peptide fragments from hen lysozyme: Insight into non-native protein conformations. Journal of Molecular Biology, 280 (4), 703-719. doi: 10.1006/jmbi.1998.1892 |
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1998 Journal Article Validation of molecular dynamics simulationvan Gunsteren, Wilfred F. and Mark, Alan E. (1998). Validation of molecular dynamics simulation. Journal of Chemical Physics, 108 (15), 6109-6116. doi: 10.1063/1.476021 |
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1998 Journal Article Parametrization of aliphatic CHn united atoms of GROMOS96 force fieldDaura, Xavier, Mark, Alan E. and van Gunsteren, Wilfred F. (1998). Parametrization of aliphatic CHn united atoms of GROMOS96 force field. Journal of Computational Chemistry, 19 (5), 535-547. doi: 10.1002/(SICI)1096-987X(19980415)19:53.0.CO;2-N |
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1997 Journal Article Liquid-liquid ion extraction: Influence of the water content of the organic phase on the ion extraction selectivity. An MD and FEP study of calix[4]crown-6 alkali cation complexes in binary chloroform-water mixturesLauterbach, M, Wipff, G, Mark, A and van Gunsteren, WF (1997). Liquid-liquid ion extraction: Influence of the water content of the organic phase on the ion extraction selectivity. An MD and FEP study of calix[4]crown-6 alkali cation complexes in binary chloroform-water mixtures. Gazzetta Chimica Italiana, 127 (11), 699-708. |
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1997 Journal Article Solvent structure at a hydrophobic protein surfaceKovacs, H, Mark, AE and vanGunsteren, WF (1997). Solvent structure at a hydrophobic protein surface. Proteins-Structure Function and Genetics, 27 (3), 395-404. doi: 10.1002/(SICI)1097-0134(199703)27:33.0.CO;2-C |
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1996 Journal Article Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactionsDaura, X, Hunenberger, PH, Mark, AE, Querol, E, Aviles, FX and vanGunsteren, WF (1996). Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions. Journal of the American Chemical Society, 118 (26), 6285-6294. doi: 10.1021/ja9537944 |
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1996 Journal Article Estimating the relative free energy of different molecular states with respect to a single reference stateLiu, HY, Mark, AE and vanGunsteren, WF (1996). Estimating the relative free energy of different molecular states with respect to a single reference state. Journal of Physical Chemistry, 100 (22), 9485-9494. doi: 10.1021/jp9605212 |
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1995 Journal Article Computer simulation of protein motionVangunsteren, WF, Hunenberger, PH, Mark, AE, Smith, PE and Tironi, IG (1995). Computer simulation of protein motion. Computer Physics Communications, 91 (1-3), 305-319. doi: 10.1016/0010-4655(95)00055-K |
