Welcome

to Vienna-PTM, a resource for exploring protein post-translational modifications (PTMs) using molecular dynamics (MD) simulations! Here, you can modify a protein PDB file of your choice with one or more supported PTMs and obtain force field parameters (GROMOS 45A3, 54A7 [ref] and 54A8 [ref]) and input files needed to perform MD simulations of the modified proteins using the GROMACS package [ref]. Currently, we support a total of 260 different enzymatic and non-enzymatic modifications.

If you use Vienna-PTM server or the associated PTM parameters for your work, please cite:

  1. Margreitter C*, Petrov D* & Zagrovic B (2013) "Vienna-PTM webserver: a toolkit for MD simulations of protein post-translational modifications" Nucleic Acids Research, 41, W422-426 [link].
  2. Petrov D*, Margreitter C*, Grandits M, Oostenbrink C & Zagrovic B (2013) "Development and verification of force-field parameters for molecular dynamics simulations of protein post-translational modifications" PLOS Computational Biology, 9(7), e1003154 [link].
  3. 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].

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