Hi,
MATLAB interfaces smoothly to Python, see the following documentation page,
Given that PyRosetta can be installed using a Python version that is compatible with a MATLAB release, then you can call MATLAB functions from it. Just take a note the compatibility of Python with MATLAB accross different releases,
MATLAB has different software solutions for the simulation and analysis of biological processes, see the following links,
There are also books regarding molecular modeling and simulation with MATLAB, see the following link for instance,
I hope this information helps.
Kind regards,
Andreas