3. Linker Molecular Weight ≤ 200 Da: this component also prevents linkers with extensive branching but more importantly, prevents the Link-INVENT agent in exploiting the weaknesses of molecular docking, e.g., generating linkers that possess a large number of HBDs which may achieve a favourable docking score but at the expense of limited permeability. See Supporting Information Fig. for the Scoring Function transformation. The binding pose of a selected generated molecule (green) superimposed with the reference ligand (gray) and the constituent fragments are circled. PDB ID: 5CU4. The structure of the generated molecule is similar to the reference ligand. The and turquoise dotted lines show the interactions formed by the reference ligand and generated ligand, respectively. The generated molecule retains the Lys68 interaction as enforced by the docking constraint and forms the same polar interactions as the reference ligand, largely attributing to the extensive overlap between the binding poses and supporting plausibility.