Hello. I was involved in a similar project some months ago. We studied the mutation by running MD simulations for both wild type (no mutations) and the mutated one. Then we performed standard trajectory analysis like RMSD to investigate any potential changes.
As far as I know, Modeller is a protein homology modelling software which is about filling missing residues using other existing experimentally derived structures of the same protein or homologs. Last time I checked it is considered to be state of the art.