Webserver / Modifying tool

  1. Margreitter C*, Petrov D* & Zagrovic B: “Vienna-PTM webserver: a toolkit for MD simulations of protein post-translational modifications” Nucleic Acids Research, 41, W422-426 (2013) [link]

Parameterization for post-translational modifications

  1. Petrov D*, Margreitter C*, Grandits M, Oostenbrink C & Zagrovic B: “Development and verification of force-field parameters for molecular dynamics simulations of protein post-translational modifications” PLOS Computational Biology, 9(7) (2013) [link]
  2. Margreitter C, Reif M & Oostenbrink C (2017) "Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field" Journal of Computational Chemistry, 38(10), 714–720 [link].

Supplements, related work

  1. Margreitter, C.: Vienna-PTM: Diploma thesis. [download]
  2. Margreitter, C.: PhD thesis (chapter 9). [download]
  3. Khoury GA, Thompson JP, Smadbeck J, Kieslich CA, and Floudas CA: “Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications” Chemical Theory and Computation, 9(12) 5653 – 5674 (2013) [link] [page]

Extended bibliography

Post-translational modifications

  1. Walsh, G. et al.: Post-translational modifications in the context of therapeutic proteins. Nature Biotechnology, 24, 1241 – 1252 (2006) [link]
  2. Walsh, Christopher T. et al.: Protein Posttranslational Modifications: The Chemistry
    of Proteome Diversifications.
    Angewandte Chemie Int. Ed., 44, 7342 – 7372 (2005) [link]

Molecular dynamics

  1. van Gunsteren, W. F. et al.: Biomolecular modeling: goals, problems, perspectives. Angewandte Chemie Int. Ed., 45, 4064 – 4092 (2006) [link]
  2. Karplus, M. et al.: Molecular dynamics simulations of biomolecules. Nature Structural Biology, 9, 646 – 652 (2002) [link]
  3. Deng, Yuqing et al.: Computations of Standard Binding Free Energies with Molecular Dynamics Simulations. Journal of Physical Chemistry B, 113(8), 2234 – 2246 (2009) [link]


  1. Lindahl, E. et al.: GROMACS 3.0: a package for molecular simulation and trajectory analysis. Journal of Molecular Modeling, 7(8), 306 – 317 (2001) [link]
  2. Van Der Spoel, D. et al.: GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701 – 1718 (2005) [link]
  3. Hess, B. et al.: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. Journal of Chemical Theory and Computation, 4(3), 435 – 447 (2008) [link]

GROMOS force fields

  1. Schuler, L. D. et al.: An Improved GROMOS96 Force Field for Aliphatic Hydrocarbons in the Condensed Phase. Journal of Computational Chemistry, 22(11), 1205 – 1218 (2001) [link]
  2. Oostenbrink, C. et al.: 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 (2004) [link]
  3. N. Schmid, A. P. Eichenberger, A. Choutko, S. Riniker, M. Winger, A. E. Mark, W.F. van Gunsteren: Definition and testing of the GROMOS force-field versions: 54A7 and 54B7 Eur. Biophys. J., 40, 843 – 856 (2011) [link]
  4. M. M. Reif, M. Winger, C. Oostenbrink: Testing of the GROMOS force-field parameter set 54A8: Structural properties of electrolyte solutions, lipid bilayers and proteins J. Chem. Theory Comput., 9, 1247 – 1264 (2013) [link]


  1. M. Christen, P. H. Hühnenberger, D. Bakowies, R. Baron, R. Bürgi, D. P. Geerke, T. N. Heinz, M. A. Kastenholz, V. Kräutler, C. Oostenbrink, C. Peter, D. Trzesniak, W. F. van Gunsteren: The GROMOS software for biomolecular simulation: GROMOS05 J. Comput. Chem., 26, 1719 – 1751 (2005) [link]
  2. N. Schmid, C. D. Christ, M. Christen, A. P. Eichenberger, W. F. van Gunsteren: Architecture, implementation and parallelization of the GROMOS software for biomolecular simulation Comp. Phys. Comm, 183, 890 – 903 (2012) [link]

Protein folding and dynamics

  1. Bowman, G. R. et al.: Taming the complexity of protein folding. Current Opinion in Structural Biology, 21(1), 4 – 11 (2011) [link]
  2. Smock, R. G. et al.: Sending Signals Dynamically. Science, 324(5924), 198 – 203 (2009) [link]
  3. Dill, K. A. et al.: The Protein Folding Problem. Annual Review of Biophysics, 37, 289 – 316 (2008) [link]

Webserver techniques

Client side

  1. Jmol: an open-source Java viewer for chemical structures in 3D. [link]
  2. Kopepasah: Eighties theme for wordpress [link]
  3. Fabien Doiron alertify.js [link]

Server side

  1. The PHP Group: Hypertext Preprocessor [link]
  2. Oracle: MySQL [link]
  3. WordPress blog software [link]
  4. Andrea Tarantini WordPress menubar plugin [link]


Group related

  1. MFPL: Max F. Perutz Laboratories [link]
  2. Group Zagrovic [link]


  1. Univie: University of Vienna [link]
  2. Meduni: Medical university of Vienna [link]
  3. BOKU: University of natural resources and Life Sciences [link]
  4. Group Oostenbrink [link]
  5. GROMOS [link]
  6. GROMACS [link]