  Molecular docking is an essential step in the drug discovery process
involving the detection of three-dimensional poses of a ligand inside the
active site of the protein. In this paper, we address the Molecular Docking
search phase by formulating the problem in QUBO terms, suitable for an
annealing approach. We propose a problem formulation as a weighted subgraph
isomorphism between the ligand graph and the grid of the target protein pocket.
In particular, we applied a graph representation to the ligand embedding all
the geometrical properties of the molecule including its flexibility, and we
created a weighted spatial grid to the 3D space region inside the pocket.
Results and performance obtained with quantum annealers are compared with
classical simulated annealing solvers.
