And you will see that in most cases nothing changes in the environment if a point mutation is introduced. So all a good mutation prediction program should do is find the best rotamer for the newly introduced residue. Now this time I was expecting much. Phe was replaced The rule that a mutated residue 'takes care of things itself' also hold for buried residues as the Filippis study makes beautifully clear. What I want to ask is that whether the Be aware that differences in observed stability is not the result of differences in structure, but of differences in the equilibrium between the folded and the unfolded form of the protein.
Refining makes things more difficult.
Your strategy is correct, assuming you used the position specific rotamer options to position the new side chain. Like described above, the structural changes that result from ligand binding are unpredictable. The averag rational drug design specialist in any pharmaceutical industry can easily explain to you why. But the docking section of the second CASP competition is also highly illustrative. That is NOT a good idea.