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2006 Journal Article Conformational polymorphism of the PrP106-126 peptide in different environments: A molecular dynamics studyVilla, A., Mark, A. E., Saracino, G. A. A., Cosentino, U., Pitea, D., Moro, G and Salmona, M. (2006). Conformational polymorphism of the PrP106-126 peptide in different environments: A molecular dynamics study. Journal of Physical Chemistry B, 110 (3), 1423-1428. doi: 10.1021/jp052722o |
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2006 Journal Article Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detailKnecht, V., Mark, A. E. and Marrink, S. J. (2006). Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail. Journal of The American Chemical Society, 128 (6), 2030-2034. doi: 10.1021/ja056619a |
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2006 Journal Article The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditionsWassenaar, T. A. and Mark, A. E. (2006). The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. Journal of Computational Chemistry, 27 (3), 316-325. doi: 10.1002/jcc.20341 |
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2006 Journal Article The role of histidine residues in low-pH-mediated viral membrane fusionKampmann, Thorsten, Meuller, Daniela S., Mark, Alan E., Young, Paul R. and Kobe, Bostjan (2006). The role of histidine residues in low-pH-mediated viral membrane fusion. Structure, 14 (10), 1481-1487. doi: 10.1016/j.str.2006.07.011 |
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2006 Journal Article Antimicrobial peptides in actionLeontiadou, H., Mark, A. E. and Marrink, S. J. (2006). Antimicrobial peptides in action. Journal of The American Chemical Society, 128 (37) acsinfecdis.7b00123, 12156-12161. doi: 10.1021/ja062927q |
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2005 Journal Article A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitationsPineiro, A., Villa, A., Vagt, T., Koksch, B. and Mark, A. E. (2005). A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations. Biophysical Journal, 89 (6), 3701-3713. doi: 10.1529/biophysj.104.055590 |
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2005 Journal Article Calculation of the redox potential of the protein azurin and some mutantsvan den Bosch, M., Swart, M., Snijders, J. G., Berendsen, H. J. C., Mark, A. E., Oostenbrink, C., van Gunsteren, W. F. and Canters, G. W. (2005). Calculation of the redox potential of the protein azurin and some mutants. Chembiochem, 6 (4), 738-746. doi: 10.1002/cbic.200400244 |
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2005 Journal Article A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: The role of Na+ ions in stabilizing the active siteKovalskyy, D., Dubyna, V., Mark, A. E. and Kornelyuk, A. (2005). A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: The role of Na+ ions in stabilizing the active site. Proteins-structure Function And Bioinformatics, 58 (2), 450-458. doi: 10.1002/prot.20304 |
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2005 Journal Article Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptidePagel, K., Seeger, K., Seiwert, B., Villa, A., Mark, A. E., Berger, S. and Koksch, B. (2005). Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide. Organic & Biomolecular Chemistry, 3 (7), 1189-1194. doi: 10.1039/b418167k |
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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 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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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 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 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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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 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 |
