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arXiv · 2503.04239

Quantum Approximate Optimization Algorithms for Molecular Docking

Christos Papalitsas·Yanfei Guan·Shreyas Waghe·Athanasios Liakos·Ioannis Balatsos·Vassilios Pantazopoulos
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Abstract

Molecular docking is a critical process for drug discovery and challenging due to the complexity and size of biomolecular systems, where the optimal binding configuration of a drug to a target protein is determined. Hybrid classical-quantum computing techniques offer a novel approach to address these challenges. The Quantum Approximate Optimization Algorithm (QAOA) and its variations are hybrid classical-quantum techniques, and a promising tool for combinatorial optimization challenges. This paper presents a Digitized Counterdiabatic QAOA (DC-QAOA) approach to molecular docking. Simulated quantum runs were conducted on a GPU cluster. We examined 14 and 17 nodes instances - to the best of our knowledge the biggest published instance is 12-node at Ding et al. and we present the results. Based on computational results, we conclude that binding interactions represent the anticipated exact solution. Additionally, as the size of the examined instance increases, the computational times exhibit a significant escalation.

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Christos Papalitsas, Yanfei Guan, Shreyas Waghe, Athanasios Liakos, Ioannis Balatsos, Vassilios Pantazopoulos. 2025-03-06. Quantum Approximate Optimization Algorithms for Molecular Docking. https://arxiv.org/abs/2503.04239

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