The development of new computational tools, such as molecular docking tools, that model and foretell the binding mode of molecular glue-induced PPI complexes, is proving to be a valuable advancement for identifying novel compatible E3 ligase-target protein partners through virtual screening and in the structure-based rational design of new optimized molecular glues. However, the application of these tools depends on a thorough structural understanding of the chemistry at the dimer interface and how a molecular glue stabilizes dimerization with the target protein, while reducing off-target binding. Moreover, better understanding of the minimal degrons necessary for PPI and small molecule protein interactions at the interface can inform the development of artificial intelligence technologies beneficial for upgrading the efficiency of data mining and molecular design.