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Scaffold hopping is a drug discovery strategy to generate new chemicalentities by modifying the core structure, the \emph{scaffold}, of a knownactive compound. This approach preserves the essential molecular features ofthe original scaffold while introducing novel chemical elements or structuralfeatures to enhance potency, selectivity, or bioavailability. However, there iscurrently a lack of generative models specifically tailored for this task,especially in the pocket-conditioned context. In this work, we presentDiffHopp, a conditional E(3)-equivariant graph diffusion model tailored forscaffold hopping given a known protein-ligand complex.

DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping