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2005 Journal Article Comparative study of generalized Born models: Protein dynamicsFan, Hao, Mark, Alan E., Zhu, Jiang and Honig, Barry (2005). Comparative study of generalized Born models: Protein dynamics. Proceedings of The National Academy of Sciences of The United States of America, 102 (19), 6760-6764. doi: 10.1073/pnas.0408857102 |
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2005 Journal Article Simulation studies of pore and domain formation in a phospholipid monolayerKnecht, V., Muller, M., Bonn, M., Marrink, S. J. and Mark, A. E. (2005). Simulation studies of pore and domain formation in a phospholipid monolayer. Journal of Chemical Physics, 122 (2) 024704, 024704.1-024704.9. doi: 10.1063/1.1825992 |
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2005 Journal Article GROMACS: Fast, flexible, and freeVan der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E. and Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26 (16), 1701-1718. doi: 10.1002/jcc.20291 |
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2005 Journal Article Molecular structure of the lecithin ripple phasede Vries, Alex H., Yefimov, Serge, Mark, Alan E. and Marrink, Siewert J. (2005). Molecular structure of the lecithin ripple phase. Proceedings of The National Academy of Sciences of The United States of America, 102 (15), 5392-5396. doi: 10.1073/pnas.0408249102 |
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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 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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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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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 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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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 |
