Literature

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]

GROMACS

  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]

GROMOS

  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. http://www.jmol.org/ [link]
  2. Kopepasah: Eighties theme for wordpress http://eighties.me [link]
  3. Fabien Doiron alertify.js http://fabien-d.github.io/alertify.js [link]

Server side

  1. The PHP Group: Hypertext Preprocessor http://www.php.net/ [link]
  2. Oracle: MySQL http://www.mysql.com/ [link]
  3. WordPress.org WordPress blog software http://www.wordpress.org [link]
  4. Andrea Tarantini WordPress menubar plugin http://wordpress.org/plugins/menubar [link]

Links

Group related

  1. MFPL: Max F. Perutz Laboratories http://www.mfpl.ac.at/ [link]
  2. Group Zagrovic [link]

Others

  1. Univie: University of Vienna http://www.univie.ac.at/ [link]
  2. Meduni: Medical university of Vienna http://www.meduniwien.ac.at/ [link]
  3. BOKU: University of natural resources and Life Sciences http://www.boku.ac.at/ [link]
  4. Group Oostenbrink [link]
  5. GROMOS [link]
  6. GROMACS [link]