What tools would one recommend for assessing the functional impact of a Non synonymous mutation on a known crystal structure. My method so far is to completely digest the literature available, and then use Modeller or I-Tasser to predict ab initio changes and then try put the pieces together. I need to be able to say things like " Amino acid 1 can no longer Hbond amino acid 5, or disulfide bridge between amino acids 5 and 10 is no longer feasible..... ligand binding pocket A is predicted to have lower binding potential.

I know these are not easy questions to answer, and certainly not definitive, but I think a reliable prediction of the structural changes caused by a mutant is a good place to start. Any suggestions would be very helpful!