![]() ![]() How to use Vienna-PTM?Īs input for subsequent simulations etc., a PDB file with post-translationally modified amino acids has to be generated by the server. New atoms are attached with pre-minimized coordinates, while energy minimization gives them a proper local orientation with respect to the whole structure. The server also makes available force field parameters needed to run MD simulations of the modified protein within the framework of the widely used GROMOS 45A3 and 54A7 force fields and GROMACS simulation package.įigure 1: Illustration of the modification workflow: A initial PDB structure, B post-translationally modified structure and C energy-minimized structure including water molecules which have been added. The Vienna-PTM webserver provides an automated procedure for introducing PTMs of choice to a user-supplied protein 3D structure (PDB file) with 259 different enzymatic and non-enzymatic modifications currently available, including phosphorylation, acetylation, methylation, hydroxylation, carbonylation and other PTMs. From enzymatic activation to cell-cycle control to transcription and translation regulation, PTMs of proteins play a key role in different cellular processes by directly affecting protein structure, dynamics and interaction networks ( YL Deribe et al., Nat. However, amino acids in proteins are frequently exposed to different enzymatic and non-enzymatic post-translational modifications (PTMs), which can completely alter their chemical nature and even affect the structure and/or dynamics of the whole protein. The basic building blocks of proteins are the 20 canonical amino acids. Background or “What is Vienna-PTM all about?” ![]()
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