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2005 Journal Article Incorporating the effect of ionic strength in free energy calculations using explicit ionsDonnini, S., Mark, A. E., Juffer, A. H. and Villa, A. (2005). Incorporating the effect of ionic strength in free energy calculations using explicit ions. Journal of Computational Chemistry, 26 (2), 115-122. doi: 10.1002/jcc.20156 |
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2005 Journal Article Simulation of gel phase formation and melting in lipid bilayers using a coarse grained modelMarrink, S. J., Risselada, J. and Mark, A. E. (2005). Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chemistry And Physics of Lipids, 135 (2), 223-244. doi: 10.1016/j.chemphyslip.2005.03.001 |
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2005 Journal Article Stability of SIV gp32 fusion-peptide single-layer protofibrils as monitored by molecular-dynamics simulationsSoto, P., Cladera, J., Mark, A. E. and Daura, X. (2005). Stability of SIV gp32 fusion-peptide single-layer protofibrils as monitored by molecular-dynamics simulations. Angewandte Chemie-international Edition, 44 (7), 1065-1067. doi: 10.1002/anie.200461935 |
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2005 Conference Publication Simulation studies of self-organization in lipid systemsKnecht, V, Marrink, SJ and Mark, AE (2005). Simulation studies of self-organization in lipid systems. 49th Annual Meeting of the Biopysical-Society, Long Beach Ca, Feb 12-16, 2005. BETHESDA: BIOPHYSICAL SOCIETY. |
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2004 Journal Article Molecular View of Hexagonal Phase Formation in Phospholipid MembranesMarrink, S. J. and Mark, A. E. (2004). Molecular View of Hexagonal Phase Formation in Phospholipid Membranes. Biophysical Journal, 87 (6), 3894-3900. doi: 10.1529/biophysj.104.048710 |
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2004 Journal Article A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6Oostenbrink, C., Villa, A., Mark, A. E. and Van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25 (13), 1656-1676. doi: 10.1002/jcc.20090 |
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2004 Journal Article Molecular dynamics simulations of hydrophilic pores in lipid bilayersLeontiadou, H., Mark, A. E. and Marrink, S. J. (2004). Molecular dynamics simulations of hydrophilic pores in lipid bilayers. Biophysical Journal, 86 (4), 2156-2164. doi: 10.1016/S0006-3495(04)74275-7 |
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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 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 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 Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detailde Vries, A. H., Mark, A. E. and Marrink, S. J. (2004). Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail. Journal of The American Chemical Society, 126 (14), 4488-4489. doi: 10.1021/ja0398417 |
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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 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 |
