Emanuele Triuzzi, Riccardo Mengoni, Francesco Micucci, Domenico Bonanni, Daniele Ottaviani, Andrea Rosario Beccari and Gianluca Palermo
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引用次数: 0
Abstract
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 quadratic unconstrained binary optimization 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. The proposed quantum annealing-based method for molecular docking achieves valid ligand placements. Compared to simulated annealing, quantum solvers sampled fewer but higher-quality solutions with lower root-mean-square deviation, demonstrating competitive performance within hardware limits.
期刊介绍:
Driven by advances in technology and experimental capability, the last decade has seen the emergence of quantum technology: a new praxis for controlling the quantum world. It is now possible to engineer complex, multi-component systems that merge the once distinct fields of quantum optics and condensed matter physics.
Quantum Science and Technology is a new multidisciplinary, electronic-only journal, devoted to publishing research of the highest quality and impact covering theoretical and experimental advances in the fundamental science and application of all quantum-enabled technologies.