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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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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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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. II. Proton transfer initiates conformational changesGroenhof, G., Lensink, M. F., Berendsen, H. J. C. and Mark, A. E. (2002). Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes. Proteins-structure Function And Genetics, 48 (2), 212-219. doi: 10.1002/prot.10135 |
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2002 Journal Article Entropy calculations on the molten globule state of a protein: Side-chain entropies of alpha-lactalbuminSchafer, H., Smith, L. J., Mark, A. E. and van Gunsteren, W. F. (2002). Entropy calculations on the molten globule state of a protein: Side-chain entropies of alpha-lactalbumin. Proteins-structure Function And Genetics, 46 (2), 215-224. doi: 10.1002/prot.1166 |
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2002 Journal Article Folding and stability of the three-stranded beta-sheet peptide betanova: Insights from molecular dynamics simulationsColombo, G., Roccatano, D. and Mark, A. E. (2002). Folding and stability of the three-stranded beta-sheet peptide betanova: Insights from molecular dynamics simulations. Proteins-structure Function And Genetics, 46 (4), 380-392. doi: 10.1002/prot.1175 |
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2002 Journal Article Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics studyRoccatano, D., Colombo, G., Fioroni, M. and Mark, A. E. (2002). Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study. Proceedings of The National Academy of Sciences of The United States of America, 99 (19), 12179-12184. doi: 10.1073/pnas.182199699 |
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2002 Journal Article A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptidesFeenstra, K. A., Peter, C., Scheek, R. M., van Gunsteren, W. F. and Mark, A. E. (2002). A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides. Journal of Biomolecular Nmr, 23 (3), 181-194. doi: 10.1023/A:1019854626147 |
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2002 Journal Article Calculation of the free energy of solvation for neutral analogs of amino acid side chainsVilla, A. and Mark, A. E. (2002). Calculation of the free energy of solvation for neutral analogs of amino acid side chains. Journal of Computational Chemistry, 23 (5), 548-553. doi: 10.1002/jcc.10052 |
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2002 Journal Article Computation of free energyvan Gunsteren, W. F., Daura, X. and Mark, A. E. (2002). Computation of free energy. Helvetica Chimica Acta, 85 (10), 3113-3129. |
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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 |
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2002 Journal Article The effect of the neglect of electronic polarization in peptide folding simulationsSoto, P. and Mark, A. E. (2002). The effect of the neglect of electronic polarization in peptide folding simulations. Journal of Physical Chemistry B, 106 (49), 12830-12833. doi: 10.1021/jp026526i |
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2001 Journal Article Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulationsBurgi, R., Daura, X., Mark, A. E., Bellanda, M., Mammi, S., Peggion, E. and van Gunsteren, W. (2001). Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations. Journal of Peptide Research, 57 (2), 107-118. doi: 10.1034/j.1399-3011.2001.00793.x |
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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 |
