# Molecular Docking via Weighted Subgraph Isomorphism on Quantum Annealers

arXiv: https://arxiv.org/abs/2405.06657 · HTML: https://mlsanity.com/paper/2405.06657/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 19 Apr 2024.

## Built on by (most cited first, 1 of 1)

- [Practical Quantum CIM Empowerment via All-Domestic-Core Agentic Large Model](https://mlsanity.com/paper/2605.23934/) (2026)

## Abstract (arXiv)

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.