Recently, the application of DL-based methods to join two molecular subunits via a chemical linker has gained considerable interest. Generating suitable linkers is important for fragment-based drug discovery (FBDD) and scaffold hopping , and fundamental for the design of proteolysis targeting chimeras (PROTACs) . The former two techniques are avenues to discover and optimize novel small molecule drugs, while the latter is a relatively new therapeutic modality able to achieve targeted protein degradation. Therefore, linker design represents a relevant problem in drug discovery.