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ResearchZernike (ZIAM)

Refereed academic publications of 2007

Molecular Dynamics
  1. Andre, I., Linse, S. & Mulder, F.A.A. Residue-specific pK(a) determination of lysine and arginine side chains by indirect N-15 and C-13 NMR spectroscopy: Application to apo calmodulin. Journal of the American Chemical Society 129 (51) 15805-15813 (2007)

  2. Baoukina, S., Monticelli, L., Marrink, S.J. & Tieleman, D.P. Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations. Langmuir 23 (25) 12617-12623 (2007)

  3. Baron, R., Trzesniak, D., de Vries, A.H., Elsener, A., Marrink, S.J. & van Gunsteren, W.F. Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. Chemphyschem 8 (3) 452-461 (2007)

  4. Helgstrand, M., Mandava, C.S., Mulder, F.A.A., Liljas, A., Sanyal, S. & Akke, M. The ribosomal stalk binds to translation factors IF2, EF-Tu, EF-G and RF3 via a conserved region of the L12 C-terminal domain. Journal of Molecular Biology 365 (2) 468-479 (2007)

  5. Knecht, V. & Marrink, S.J. Molecular dynamics simulations of lipid vesicle fusion in atomic detail. Biophysical Journal 92 (12) 4254-4261 (2007)

  6. Leontiadou, H., Mark, A.E. & Marrink, S.J. Ion transport across transmembrane pores. Biophysical Journal 92 (12) 4209-4215 (2007)

  7. Lindman, S., Linse, S., Mulder, F.A.A. & Andre, I. pK(a) values for side-chain carboxyl groups of a PGB1 variant explain salt and pH-dependent stability. Biophysical Journal 92 (1) 257-266 (2007)

  8. Marrink, S.J., Risselada, H.J., Yefimov, S., Tieleman, D.P. & de Vries, A.H. The MARTINI force field: Coarse grained model for biomolecular simulations. Journal of Physical Chemistry B 111 (27) 7812-7824 (2007)

  9. Periole, X. & Mark, A.E. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. Journal of Chemical Physics 126 (1) 014903 (2007)

  10. Periole, X., Huber, T., Marrink, S.J. & Sakmar, T.P. G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. Journal of the American Chemical Society 129 (33) 10126-10132 (2007)

  11. Periole, X., Vendruscolo, M. & Mark, A.E. Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain. Proteins-Structure Function and Bioinformatics 69 (3) 536-550 (2007)

  12. Pineiro, A., Banquy, X., Perez-Casas, S., Tovar, E., Garcia, A., Villa, A., Amigo, A., Mark, A.E. & Costas, M. On the characterization of host-guest complexes: Surface tension, calorimetry, and molecular dynamics of cyclodextrins with a non-ionic surfactant. Journal of Physical Chemistry B 111 (17) 4383-4392 (2007)

  13. Siwko, M.E., Marrink, S.J., de Vries, A.H., Kozubek, A., Uiterkamp, A.J.M.S. & Mark, A.E. Does isoprene protect plant membranes from thermal shock? A molecular dynamics study. Biochimica et Biophysica Acta-Biomembranes 1768 (2) 198-206 (2007)

  14. van den Bogaart, G., Hermans, N., Krasnikov, V., de Vries, A.H. & Poolman, B. On the decrease in lateral mobility of phospholipids by sugars. Biophysical Journal 92 (5) 1598-1605 (2007)

  15. Villa, A., Fan, H., Wassenaar, T. & Mark, A.E. How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field? Journal of Physical Chemistry B 111 (21) 6015-6025 (2007)

Last modified:22 October 2012 2.29 p.m.