A Physically Informed QUBO Model for π‑Stacking Interactions in Molecular Docking Problems

Molecular docking is a computational technique central to computer-aided drug discovery (CADD), aimed at predicting the preferred binding mode and binding affinity of a small-molecule ligand within the active site of a target macromolecule. Recent advances in quantum computing have led to the development of new molecular docking models. In particular, quantum annealing has motivated the formulation of physically informed docking frameworks that can be encoded within discrete optimization paradigms such as QUBO formulations.