In conclusion, in silico protein–protein docking analyses can be used to support the described ataxin-3 interactors as true interactors, predict novel ataxin-3 interactors, predict interactor binding differences with the WT and expanded ataxin-3 forms, predict which proteins will show altered levels, and make predictions regarding the type of mitophagy observed in SCA3/MJD. This evidence concerns the gene ATXN3 and Spinocerebellar ataxia type 3.