Publications

• Mark, P., Nilsson, L.
  Molecular Dynamics Simulations of the Ala-Pro Dipeptide in Water: Conformational Dynamics of Trans and Cis Isomers Using Different Water Models.
  J. Phys. Chem. B 2001, 105, 8028-8035.
  [download pdf-file]
• Mark, P., Nilsson, L.
  Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K.
  J. Phys. Chem. A 2001, 105, 9954-9960.
  [download pdf-file]
• Mark, P., Nilsson, L.
  Structure and Dynamics of Liquid Water with Different Long-Range Interaction Truncation and Temperature Control Methods in Molecular Dynamics Simulations.
  J. Comput. Chem. 2002, 23, 1211-1219.
  [download pdf-file]
• Mark, P., Nilsson, L.
  A Molecular Dynamics Study of Tryptophan in Water.
  J. Phys. Chem. B 2002, 106, 9440-9445.
  [download pdf-file]
• Thesis: Molecular dynamics studies of water and biomolecules Pekka Mark ISBN 91-7349-251-5 (2002)
• Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C., Mark, P., Stumpflen, V., Mewes, H.W., Ruepp, A., Frishman, D.
  The MIPS mammalian protein-protein interaction database.
  Bioinformatics 2005, 21(6), 832-834.
  [download pdf-file]
• Rundgren, H., Mark, P., Laaksonen, A.
  Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution.
  J. Mol. Struc.(THEOCHEM). 2007, 810, 113-120.
  download pdf-file
• Rundgren, H., Mark, P., Laaksonen, A.
  Molecular dynamics simulations of conserved Hox protein hexapeptides. II. Folded structures in water solution.
  J. Mol. Struc.(THEOCHEM). 2007, 805, 61-70.
  download pdf-file
• Rundgren, H., Mark, P., Laaksonen, A.
  Molecular dynamics simulations of conserved Hox protein hexapeptides. III. Hydration of Hox peptides.
  Manuscript in Preparation.
  [download pdf-file]
• Mark, P., Nilsson, L.
  A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide.
  Eur Biophys J. 2007, 36(3), 213-224.
  [download pdf-file]
• Nakagawa, S., Mark, P., Agren, H.
  Recipe of Polarized One-electron Potential Optimization for Development of Polarizable Force Fields.
  J. Chem. Theory Comput. (Special Issue on Polarization) 2007, 3(6), 1947-1959.
  [download pdf-file]
• Mark, P., Baumann, M.L., Eklöf, J., Gullfot, F., Michel, G., Kallas, Å., Teeri, T.T., Brumer, H., Czjzek, M.
  Analysis of nasturtium TmNXG1 complexes by crystallography and molecular dynamics provides detailed insight into substrate recognition by family GH16 xyloglucan endo-transglycosylases and endo-hydrolases.
  Proteins: Structure, Function, and Bioinformatics 2009, 75(4), 820-836.
  [DOI: 10.1002/prot.22291]

Book chapters

• Johan Bredenberg, Pekka Mark and Lennart Nilsson
  Solvent effects on biomolecular dynamics simulations: A comparison between TIP3P, SPC and SPC/E water models acting on the Glucocorticoid receptor DNA-binding domain.
  In "Modern Methods for Theoretical Physical Chemistry of Biopolymers" Edited by E.B. Starikov, J.P. Lewis and S. Tanaka, Elsevier B.V. Amsterdam. 2006. 123-135.
  [download pdf-file]