Vienna-PTM

Vienna-PTM automates the introduction of 256 enzymatic and non-enzymatic post-translational modifications (PTMs) into protein 3D structures and provides force field parameters for molecular dynamics (MD) simulations.

Key Features:

• PTM repertoire: Introduces 256 enzymatic and non-enzymatic PTMs into protein structures.
• Input format: Accepts Protein Data Bank (PDB) files as input for target proteins.
• Site-specific modification: Implements geometrically realistic, site-specific modifications at specified residues.
• Energy minimization: Performs energy minimization after PTM introduction to improve structural stability.
• MD parameter generation: Supplies force field parameters and input files compatible with GROMOS 54A7 and 45A3 for use with the GROMACS simulation package.

Scientific Applications:

• Atomistic MD studies: Enables atomistic molecular dynamics simulations to investigate structural, dynamic, and interaction effects of PTMs.
• MD system preparation: Prepares modified proteins and simulation input parameters for GROMOS 54A7/45A3 and GROMACS workflows.
• Structural analysis of PTMs: Supports assessment of geometrical consequences and stability of site-specific PTMs via energy-minimized structures.

Methodology:

Accepts Protein Data Bank (PDB) files, introduces geometrically realistic, site-specific PTMs (256 types), performs energy minimization, and outputs force field parameters and GROMACS-compatible input files for GROMOS 54A7 and 45A3.