Papers

If you use the ViennaPTM web application, the Python library, the CLI tool, or the associated PTM parameters for your work, please cite the relevant publications below.

ViennaPTM webserver

Christian Margreitter, Drazen Petrov, and Bojan Žagrović

ViennaPTM web server: a toolkit for MD simulations of protein post-translational modifications

Nucleic Acids Research, 41(W1):W422–W426, 2013

DOI: 10.1093/nar/gkt416

GROMACS force-field parameters

Drazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, and Bojan Žagrović

A systematic framework for molecular dynamics simulations of protein post-translational modifications

PLoS Computational Biology, 9(7):e1003154, 2013

Force-field parameters for GROMACS 45A3 and 54A7

DOI: 10.1371/journal.pcbi.1003154
Christian Margreitter, Maria M. Reif, and Chris Oostenbrink

Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force-field

Journal of Computational Chemistry, 38:714–720, 2017

Updated phosphate parameters for GROMACS 54A8

DOI: 10.1002/jcc.24733

Source: ViennaPTM documentation — Citation