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ResearchZernike (ZIAM)

Refereed academic publications of 2005

Molecular Dynamics
  1. de Vries, A.H., Yefimov, S., Mark, A.E. & Marrink, S.J. Molecular structure of the lecithin ripple phase. Proceedings of the National Academy of Sciences of the United States of America 102 (15) 5392-5396 (2005)

  2. Donnini, S., Mark, A.E., Juffer, A.H. & Villa, A. Incorporating the effect of ionic strength in free energy calculations using explicit ions. Journal of Computational Chemistry 26 (2) 115-122 (2005)

  3. Fan, H., Mark, A.E., Zhu, J. & Honig, B. 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 (2005)

  4. Knecht, V., Marrink, S.J. & Mark, A.E. Simulation studies of self-organization in lipid systems. Biophysical Journal 88 (1) 384A (2005)

  5. Knecht, V., Muller, M., Bonn, M., Marrink, S.J. & Mark, A.E. Simulation studies of pore and domain formation in a phospholipid monolayer. Journal of Chemical Physics 122 (2) art. 024704 (2005)

  6. Kovalskyy, D., Dubyna, V., Mark, A.E. & Kornelyuk, A. 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 (2005)

  7. Kovalskyy, D.B., Dubina, V.M., Mark, A.E. & Kornelyuk, A.I. Effect of distal mutations on the molecular dynamics of the HIV-1 protease. Febs Journal 272 143 (2005)

  8. Lundstrom, P., Mulder, F.A.A. & Akke, M. Correlated dynamics of consecutive residues reveal transient and cooperative unfolding of secondary structure in proteins. Proceedings of the National Academy of Sciences of the United States of America 102 (47) 16984-16989 (2005)

  9. Marrink, S.J. & Mark, A.E. Coarse grained simulation of phase transitions of lipid membranes. Biophysical Journal 88 (1) 384A (2005)

  10. Marrink, S.J., Risselada, J. & Mark, A.E. Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chemistry and Physics of Lipids 135 (2) 223-244 (2005)

  11. Pagel, K., Seeger, K., Seiwert, B., Villa, A., Mark, A.E., Berger, S. & Koksch, B. Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide. Organic & Biomolecular Chemistry 3 (7) 1189-1194 (2005)

  12. Soto, P., Cladera, J., Mark, A.E. & Daura, X. Stability of SIV gp32 fusion-peptide single-layer protofibrils as monitored by molecular-dynamics simulations. Angewandte Chemie-International Edition 44 (7) 1065-1067 (2005)

  13. Spoel, D.v., Lindahl, E., Hess, B., Groenhof, G., Mark, A.E. & Berendsen, H.J.C. GROMACS: Fast, flexible and free. Journal of Computational Chemistry 26 (16) 1701-1718 (2005)

  14. van den Bosch, M., Swart, M., Snijders, J.G., Berendsen, H.J.C., Mark, A.E., Oostenbrink, C., van Gunsteren, W.F. & Canters, G.W. Calculation of the redox potential of the protein azurin and some mutants. Chembiochem 6 (4) 738-746 (2005)

Last modified:22 October 2012 2.29 p.m.