标题： 基于增强量子退火方法的分子展开公式化 显示英文标题

标题： Molecular unfolding formulation with enhanced quantum annealing approach

摘要： 分子对接是药物发现中的关键阶段，涉及精确确定两个分子结合时的最佳空间排列。 在此分析中，分子的三维结构是一个基本考虑因素，包括基于它们自由度的操作，如刚体旋转和平移以及沿可旋转键的片段旋转，以确定分子相互结合时的优选空间排列。 本文探讨了基于量子退火的分子展开（MU）问题解决方案，并将其与一种名为“GeoDock”的先进经典算法进行了比较。分子展开侧重于将一个分子扩展到未折叠状态，以便简化目标腔内的操作并优化其构象，通常通过最大化分子面积或内部原子距离来实现。 分子展开问题旨在找到增加分子内原子间距离的扭转构象，这也会增加分子面积。 量子退火方法首先将该问题编码为高阶无约束二进制优化（HUBO）方程，并修剪至任意百分比以提高时间效率，从而能够使用任何量子退火器解决该方程。 然后将所得的HUBO方程转换为二次无约束二进制优化方程（QUBO），后者可以轻松嵌入D-Wave退火量子处理器上。 显示英文摘要

摘要： Molecular docking is a crucial phase in drug discovery, involving the precise determination of the optimal spatial arrangement between two molecules when they bind. The such analysis, the 3D structure of molecules is a fundamental consideration, involving the manipulation of molecular representations based on their degrees of freedom, including rigid roto-translation and fragment rotations along rotatable bonds, to determine the preferred spatial arrangement when molecules bind to each other. In this paper, quantum annealing based solution to solve Molecular unfolding (MU) problem, a specific phase within molecular docking, is explored and compared with a state-of-the-art classical algorithm named "GeoDock". Molecular unfolding focuses on expanding a molecule to an unfolded state to simplify manipulation within the target cavity and optimize its configuration, typically by maximizing molecular area or internal atom distances. Molecular unfolding problem aims to find the torsional configuration that increases the inter-atomic distance within a molecule, which also increases the molecular area. Quantum annealing approach first encodes the problem into a Higher-order Unconstrained Binary Optimization (HUBO) equation which is pruned to an arbitrary percentage to improve the time efficiency and to be able to solve the equation using any quantum annealer. The resultant HUBO is then converted to a Quadratic Unconstrained Binary Optimization equation (QUBO), which is easily embedded on a D-wave annealing Quantum processor.