For AlphaFold2, you could use the Jupyter Notebook app, which would allow you to start a job with proper resources. Then within that you could give your users an “AlphaFold notebook”, which is prepopulated with info on how to run the program. Not sure if this would be applicable to non-Python software.
That would appear to be similar to the Colab notebook they link to on their GitHub README (Google Colab). My thought was to use something like the “Making a Prediction” section of that notebook.
We’re not doing this at our site but this is what came to mind. Good luck!