Molecular docking via weighted subgraph isomorphism on quantum annealers

IF 5 2区 物理与天体物理 Q1 PHYSICS, MULTIDISCIPLINARY
Emanuele Triuzzi, Riccardo Mengoni, Francesco Micucci, Domenico Bonanni, Daniele Ottaviani, Andrea Rosario Beccari and Gianluca Palermo
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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.
量子退火上基于加权子图同构的分子对接
分子对接是药物发现过程中必不可少的一步,涉及检测蛋白质活性位点内配体的三维姿态。在本文中,我们通过将问题表述为适合退火方法的二次型无约束二元优化项来解决分子对接搜索阶段。我们提出了一个配体图和靶蛋白口袋网格之间的加权子图同构的问题公式。特别是,我们对嵌入分子的所有几何特性(包括其灵活性)的配体应用了图形表示,并为口袋内的3D空间区域创建了加权空间网格。提出的基于量子退火的分子对接方法实现了有效的配位。与模拟退火相比,量子求解器取样更少,但质量更高,均方根偏差更低,在硬件限制下表现出竞争力。
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来源期刊
Quantum Science and Technology
Quantum Science and Technology Materials Science-Materials Science (miscellaneous)
CiteScore
11.20
自引率
3.00%
发文量
133
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.
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