ViennaPTM provides a validated toolkit for applying post-translational modifications (PTMs) to protein structures, supporting structure preparation for molecular dynamics and related simulation workflows.

The webserver offers an interactive workflow for uploading or fetching structures and selecting modifications step by step. New users are encouraged to read the Webserver Tutorial before getting started.

The backend Python library is available through the Backend menu and is suited to scripted or large-scale use. Choose the entrypoint (CLI) for quick, straightforward runs from the command line or a configuration file, or the Application Programming Interface (API) when you need greater flexibility — for example, batch processing or advanced, customised modification workflows.