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2004 Journal Article Refinement of homology-based protein structures by molecular dynamics simulation techniquesFan, H. and Mark, A. E. (2004). Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Science, 13 (1), 211-220. doi: 10.1110/ps.03381404 |
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2004 Journal Article Electrofreezing of confined waterZangi, R. and Mark, A. E. (2004). Electrofreezing of confined water. Journal of Chemical Physics, 120 (15), 7123-7130. doi: 10.1063/1.1687315 |
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2004 Journal Article Coarse grained model for semiquantitative lipid simulationsMarrink, S. J., de Vries, A. H. and Mark, A. E. (2004). Coarse grained model for semiquantitative lipid simulations. Journal of Physical Chemistry B, 108 (2), 750-760. doi: 10.1021/jp036508g |
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2004 Journal Article Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structuresFan, H. and Mark, A. E. (2004). Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures. Protein Science, 13 (4), 992-999. doi: 10.1110/ps.03449904 |
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2004 Journal Article Photoactivation of the photoactive yellow protein: Why photon absorption triggers a trans-to-cis lsomerization of the chromophore in the proteinGroenhof, G., Bouxin-Cademartory, M., Hess, B., De Visser, S. P., Berendsen, H. J. C., Olivucci, M., Mark, A. E. and Robb, M. A. (2004). Photoactivation of the photoactive yellow protein: Why photon absorption triggers a trans-to-cis lsomerization of the chromophore in the protein. Journal of The American Chemical Society, 126 (13), 4228-4233. doi: 10.1021/ja039557f |
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2004 Journal Article The binary mixing behavior of phospholipids in a bilayer: A molecular dynamics studyde Vries, A. H., Mark, A. E. and Marrink, S. J. (2004). The binary mixing behavior of phospholipids in a bilayer: A molecular dynamics study. Journal of Physical Chemistry B, 108 (7), 2454-2463. doi: 10.1021/jp0366926 |
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2003 Journal Article Monolayer iceZangi, R. and Mark, A. E. (2003). Monolayer ice. Physical Review Letters, 91 (2) 025502, 025502-1-025502-4. doi: 10.1103/PhysRevLett.91.025502 |
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2003 Journal Article Simulation of MscL Gating in a Bilayer under StressColombo, G., Marrink, S. J. and Mark, A. E. (2003). Simulation of MscL Gating in a Bilayer under Stress. Biophysical Journal, 84 (4), 2331-2337. doi: 10.1016/S0006-3495(03)75038-3 |
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2003 Journal Article Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation studyFan, H. and Mark, A. E. (2003). Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study. Proteins-structure Function And Genetics, 53 (1), 111-120. doi: 10.1002/prot.10496 |
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2003 Journal Article Simulation of pore formation in lipid bilayers by mechanical stress and electric fieldsTieleman, D. P., Leontiadou, H., Mark, A. E. and Marrink, S. J. (2003). Simulation of pore formation in lipid bilayers by mechanical stress and electric fields. Journal of The American Chemical Society, 125 (21), 6382-6383. doi: 10.1021/ja029504i |
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2003 Journal Article Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsinVilla, A., Zangi, R., Pieffet, G. and Mark, A. E. (2003). Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin. Journal of Computer-aided Molecular Design, 17 (10), 673-686. doi: 10.1023/B:JCAM.0000017374.53591.32 |
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2003 Journal Article The mechanism of vesicle fusion as revealed by molecular dynamics simulationsMarrink, S. J. and Mark, A. E. (2003). The mechanism of vesicle fusion as revealed by molecular dynamics simulations. Journal of The American Chemical Society, 125 (37), 11144-11145. doi: 10.1021/ja036138+ |
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2003 Journal Article Understanding binding affinity: A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsinTalhout, R., Villa, A., Mark, A. E. and Engberts, J. B. F. N. (2003). Understanding binding affinity: A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin. Journal of The American Chemical Society, 125 (35), 10570-10579. doi: 10.1021/ja034676g |
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2003 Journal Article The influence of trifluoromethyl groups on the miscibility of fluorinated alcohols with water: A molecular dynamics simulation study of 1,1,1-trifluoropropan-2-ol in aqueous solutionFioroni, M., Burger, K., Mark, A. E. and Roccatano, D. (2003). The influence of trifluoromethyl groups on the miscibility of fluorinated alcohols with water: A molecular dynamics simulation study of 1,1,1-trifluoropropan-2-ol in aqueous solution. Journal of Physical Chemistry B, 107 (20), 4855-4861. doi: 10.1021/jp026076u |
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2003 Journal Article Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesiclesMarrink, Siewert J. and Mark, Alan E. (2003). Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. Journal of The American Chemical Society, 125 (49), 15233-15242. doi: 10.1021/ja0352092 |
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2003 Journal Article Bilayer ice and alternate liquid phases of confined waterZangi, R. and Mark, A. E. (2003). Bilayer ice and alternate liquid phases of confined water. Journal of Chemical Physics, 119 (3), 1694-1700. doi: 10.1063/1.1580101 |
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2002 Journal Article Molecular Dynamics Study of the Folding of Hydrophobin SC3 at a Hydrophilic/Hydrophobic InterfaceZangi, R., de Vocht, M. L., Robillard, G. T. and Mark, A. E. (2002). Molecular Dynamics Study of the Folding of Hydrophobin SC3 at a Hydrophilic/Hydrophobic Interface. Biophysical Journal, 83 (1), 112-124. doi: 10.1016/S0006-3495(02)75153-9 |
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2002 Journal Article Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophoreGroenhof, G., Lensink, M. F., Berendsen, H. J. C., Snijders, J. G. and Mark, A. E. (2002). Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore. Proteins-structure Function And Genetics, 48 (2), 202-211. doi: 10.1002/prot.10136 |
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2002 Journal Article Dynamic conformations of flavin adenine dinucleotide: Simulated molecular dynamics of the flavin cofactor related to the time-resolved fluorescence characteristicsvan den Berg, P. A. W., Feenstra, K. A., Mark, A. E., Berendsen, H. J. C. and Visser, A. J. W. G. (2002). Dynamic conformations of flavin adenine dinucleotide: Simulated molecular dynamics of the flavin cofactor related to the time-resolved fluorescence characteristics. Journal of Physical Chemistry B, 106 (34), 8858-8869. doi: 10.1021/jp020356s |
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2002 Journal Article Molecular dynamics simulations of mixed micelles modeling human bileMarrink, S. J. and Mark, A. E. (2002). Molecular dynamics simulations of mixed micelles modeling human bile. Biochemistry, 41 (17), 5375-5382. doi: 10.1021/bi015613i |
