8.4 years ago by
Stanford University, U
Modeller isn't likely to give you any hints. Since it's homology modelling, the entire protein, bar the mutation(s), is going to retain exactly the same structural features. Rosetta Backrub does seem a much better alternative for this.
If you can, get your hands on a MD package like GROMACS and run a moderately long simulation, depending on the size of your protein, so you can derive some conclusions out of it, although you won't see any spectacular unfolding or rearrangement. This will take a bit more time (a few days running, another few analyzing the results) but will probably give you a much more detailed picture of the influence of the mutations in the dynamics of the protein.
In the case of protein-protein complexes, I would look at the latest rounds of CAPRI and decide on who to choose to model the complex.