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2006 Journal Article Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structuresFan, Hao and Mark, Alan E. (2006). Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures. Protein Science, 15 (3), 441-448. doi: 10.1110/ps.051721006 |
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2006 Conference Publication The mechanism of vira membrane fusion and identification of novel antiviral lead compoundsKampmann, T., Muller,, Robinson, J., Mark, A, Young, P R and Kobe, B (2006). The mechanism of vira membrane fusion and identification of novel antiviral lead compounds. 31st Lorne Conference on Protein Structure & Function, Lorne, Victoria, Australia, 5-9 Feb, 2006. |
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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 Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interfaceFan, Hao, Wang, Xiaoqin, Zhu, Jiang, Robillard, George T. and Mark, Alan E. (2006). Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface. Proteins-structure Function And Bioinformatics, 64 (4), 863-873. doi: 10.1002/prot.20936 |
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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 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 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 Conference Publication Simulations of phase transformations of lipid-water mixtures by molecular dynamicsde Vries, AH, Knecht, V, Yefimov, S, Mark, AE and Marrink, SI (2005). Simulations of phase transformations of lipid-water mixtures by molecular dynamics. 230th National Meeting of the American-Chemical-Society, Washington Dc, Aug 28-Sep 01, 2005. WASHINGTON: AMER CHEMICAL SOC. |
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2005 Conference Publication Effect of distal mutations on the molecular dynamics of the HIV-1 proteaseKovalskyy, DB, Dubina, VM, Mark, AE and Kornelyuk, AI (2005). Effect of distal mutations on the molecular dynamics of the HIV-1 protease. IUBMB 50th Anniversary Symposium, Budapest Hungary, Jul 02-07, 2005. OXFORD: BLACKWELL PUBLISHING. |
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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 Conference Publication A structural model for low pH mediated viral fusion: The role of histidine protonationKampmann, T., Muller, D. A., Robinson, J., Mark, A., Young, P. R. and Kobe, B. (2005). A structural model for low pH mediated viral fusion: The role of histidine protonation. 3rd Australian Virology Group Meeting, Phillip Island, 9-12 Dec, 2005. |
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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 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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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 |
