Quantum molecular unfolding
Quantum molecular unfolding
复制标题
DOI：
10.1088/2058-9565/ac73af
复制
发表时间：
2022-07-01
影响因子：
6.7
通讯作者：
Palermo, Gianluca
中科院分区：
文献类型：
--
作者：
Mato, Kevin;Mengoni, Riccardo;Palermo, Gianluca
分子对接是药物发现过程中的一个重要步骤，其目的是计算一个分子与另一个分子结合时的优选位置和形状。在这样的分析过程中，分子的3D表示根据它们的自由度进行操作：刚性旋转平移和片段旋转沿着可旋转键。在我们的工作中，我们专注于分子对接过程的一个特定阶段，即分子解折叠（MU），其用于通过将分子扩展到更容易在靶腔内操作的解折叠形状来去除分子的初始偏差。MU问题的目标是找到最大化分子面积的构型，或者等价地，最大化分子内部原子之间的内部距离。我们提出了一种量子退火方法，通过将其制定为高阶无约束二进制优化，可以在最新的D波退火硬件（2000 Q和优势）上解决。与量子退火机获得的结果和性能进行比较与最先进的经典求解器。
Molecular docking is an important step of the drug discovery process which aims at calculating the preferred position and shape of one molecule to a second when they are bound to each other. During such analysis, 3D representations of molecules are manipulated according to their degree of freedoms: rigid roto-translation and fragment rotations along the rotatable bonds. In our work, we focussed on one specific phase of the molecular docking procedure i.e. molecular unfolding (MU), which is used to remove the initial bias of a molecule by expanding it to an unfolded shape simpler to manipulate within the target cavity. The objective of the MU problem is to find the configuration that maximizes the molecular area, or equivalently, that maximizes the internal distances between atoms inside the molecule. We propose a quantum annealing approach to MU by formulating it as a high-order unconstrained binary optimization which was possible to solve on the latest D-wave annealing hardware (2000Q and advantage). Results and performances obtained with quantum annealers are compared with state of art classical solvers.