Scaffold hopping refers to modifying the core structure of a molecule to improve physicochemical properties while retaining potency. The task can be formulated as a linker design problem if the scaffold itself is defined as the linker between two molecular subunits. Scaffold hopping is challenging as retaining potency requires 3D structural awareness of the interactions formed between the molecule and its receptor. Similar to fragment linking, improvements in linker design can enhance the ability to generate novel scaffold ideas.