Journal Article

Efficient molecular conformation generation with quantum-inspired algorithm

Zhu, Huangjun, Wang, Bi-Ying, Qiao, Nan, Yung, Man-Hong, Shu, Runqiu, Cui, Xiaopeng, Xiong, Zhaoping, Liu, Bowen, Li, Yunting, Zou, Zuoheng

2024

Overview

Context Conformation generation, also known as molecular unfolding (MU), is a crucial step in structure-based drug design, remaining a challenging combinatorial optimization problem. Quantum annealing (QA) has shown great potential for solving certain combinatorial optimization problems over traditional classical methods such as simulated annealing (SA). However, a recent study showed that a 2000-qubit QA hardware was still unable to outperform SA for the MU problem. Here, we propose the use of quantum-inspired algorithm to solve the MU problem, in order to go beyond traditional SA. We introduce a highly compact phase encoding method which can exponentially reduce the representation space, compared with the previous one-hot encoding method. For benchmarking, we tested this new approach on the public QM9 dataset generated by density functional theory (DFT). The root-mean-square deviation between the conformation determined by our approach and DFT is negligible (less than about 0.5Å), which underpins the validity of our approach. Furthermore, the median time-to-target metric can be reduced by a factor of five compared to SA. Additionally, we demonstrate a simulation experiment by MindQuantum using quantum approximate optimization algorithm (QAOA) to reach optimal results. These results indicate that quantum-inspired algorithms can be applied to solve practical problems even before quantum hardware becomes mature. Methods The objective function of MU is defined as the sum of all internal distances between atoms in the molecule, which is a high-order unconstrained binary optimization (HUBO) problem. The degree of freedom of variables is discretized and encoded with binary variables by the phase encoding method. We employ the quantum-inspired simulated bifurcation algorithm for optimization. The public QM9 dataset is generated by DFT. The simulation experiment of quantum computation is implemented by MindQuantum using QAOA.

• Publisher: Springer Berlin Heidelberg,Springer Nature B.V
• Subject: Algorithms / Bifurcations / Characterization and Evaluation of Materials / Chemical bonds / Chemistry / Chemistry and Materials Science / Coding / Combinatorial analysis / Computer Appl. in Life Sciences / Computer Applications in Chemistry / Conformation / data collection / Datasets / Density functional theory / drug design / Drug development / Hardware / Ligands / Linear algebra / Molecular conformation / Molecular Medicine / Optimization / Original Paper / Quantum computing / Qubits (quantum computing) / Simulated annealing / system optimization / Theoretical and Computational Chemistry