I am trying to model Opa3 which is a protein in the mitochondria. There is evidence showing that when this protein is mutated there is a build up of 3-methylglutaconic aciduria, type 3 (MGA-3). We are trying to find a ligand that is in the pathway of production/breakdown of this compound so we can mutate the amino acids the ligand would bind to. Because of the unique conditions in the mitochondria I don't really know where to start in predicting a stable model and a ligand binding site. Any suggestions or advice on what tools or programs to use?