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2001 Journal Article Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulationRoccatano, D., Mark, A. E. and Hayward, S. (2001). Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation. Journal of Molecular Biology, 310 (5), 1039-1053. doi: 10.1006/jmbi.2001.4808 |
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2001 Journal Article Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bondsde Groot, B. L., Daura, X., Mark, A. E. and Grubmuller, H. (2001). Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds. Journal of Molecular Biology, 309 (1), 299-313. doi: 10.1006/jmbi.2001.4655 |
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2001 Journal Article Simulation of the spontaneous aggregation of phospholipids into bilayersMarrink, S. J., Lindahl, E., Edholm, O. and Mark, A. E. (2001). Simulation of the spontaneous aggregation of phospholipids into bilayers. Journal of The American Chemical Society, 123 (35), 8638-8639. doi: 10.1021/ja0159618 |
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2001 Journal Article Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behaviorSchafer, H., Daura, X., Mark, A. E. and van Gunsteren, W. F. (2001). Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior. Proteins-structure Function And Genetics, 43 (1), 45-56. doi: 10.1002/1097-0134(20010401)43:13.0.CO;2-N |
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2001 Journal Article Effect of undulations on surface tension in simulated bilayersMarrink, S. J. and Mark, A. E. (2001). Effect of undulations on surface tension in simulated bilayers. Journal of Physical Chemistry B, 105 (26), 6122-6127. doi: 10.1021/jp0103474 |
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2000 Journal Article Molecular dynamics simulation of the kinetics of spontaneous micelle formationMarrink, S. J., Tieleman, D. P. and Mark, A. E. (2000). Molecular dynamics simulation of the kinetics of spontaneous micelle formation. Journal of Physical Chemistry B, 104 (51), 12165-12173. doi: 10.1021/jp001898h |
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2000 Journal Article A new 2,2,2-triflouroethanol model for molecular dynamics simulationsFioroni, Marco, Burger, Klaus, Mark, Alan E. and Roccatano, Danilo (2000). A new 2,2,2-triflouroethanol model for molecular dynamics simulations. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 104 (51), 12347-12354. doi: 10.1021/jp002115v |
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2000 Journal Article Absolute entropies from molecular dynamics simulation trajectoriesSchafer, Heiko, Mark, Alan E. and van Gunsteren, Wilfred F. (2000). Absolute entropies from molecular dynamics simulation trajectories. Journal of Chemical Physics, 113 (18), 7809-7817. doi: 10.1063/1.1309534 |
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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 |
