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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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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 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 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 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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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 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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2001 Journal Article Further investigation on the validity of Stokes-Einstein behaviour at the molecular levelWalser, R., Hess, B., Mark, A. E. and van Gunsteren, W. F. (2001). Further investigation on the validity of Stokes-Einstein behaviour at the molecular level. Chemical Physics Letters, 334 (4-6), 337-342. doi: 10.1016/S0009-2614(00)01290-2 |
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2001 Journal Article Model of 1,1,1,3,3,3-hexafluoro-propan-2-ol for molecular dynamics simulationsFioroni, M., Burger, K., Mark, A. E. and Roccatano, D. (2001). Model of 1,1,1,3,3,3-hexafluoro-propan-2-ol for molecular dynamics simulations. Journal of Physical Chemistry B, 105 (44), 10967-10975. doi: 10.1021/jp012476q |
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2001 Journal Article Free energy barrier estimation of unfolding the alpha-helical surfactant-associated polypeptide CZangi, R., Kovacs, H., van Gunsteren, W. F., Johansson, J. and Mark, A. E. (2001). Free energy barrier estimation of unfolding the alpha-helical surfactant-associated polypeptide C. Proteins-structure Function And Genetics, 43 (4), 395-402. doi: 10.1002/prot.1052 |
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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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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 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 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 |
