Molecular Docking via Weighted Subgraph Isomorphism on Quantum Annealers
It provides a novel quantum annealing approach for the molecular docking search phase in drug discovery, though performance is only comparable to classical methods.
The paper formulates molecular docking as a weighted subgraph isomorphism problem solvable on quantum annealers, achieving results comparable to classical simulated annealing solvers.
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.