Efficient molecular conformation generation with quantum-inspired algorithm

Li, Yunting1,2; Cui, Xiaopeng2; Xiong, Zhaoping3; Zou, Zuoheng2; Liu, Bowen2; Wang, Bi-Ying2; Shu, Runqiu2; Zhu, Huangjun1; Qiao, Nan3; Yung, Man-Hong2,4,5,6,7,8

2024-07-01

10.1007/s00894-024-05962-9

JOURNAL OF MOLECULAR MODELING   影响因子和分区

1610-2940

0948-5023

ContextConformation 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 0.5 & Aring;), 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.MethodsThe 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.

Drug design Molecular conformation generation Molecular unfolding Molecular docking Quantum annealing Quantum-inspired

SCI

英语

通讯

Biochemistry & Molecular Biology ; Biophysics ; Chemistry ; Computer Science

Biochemistry & Molecular Biology ; Biophysics ; Chemistry, Multidisciplinary ; Computer Science, Interdisciplinary Applications

WOS:001254814500001

SPRINGER

CHEMISTRY

Web of Science

1.Fudan Univ, Inst Nanoelect Devices & Quantum Comp, Shanghai 200433, Peoples R China
2.Huawei Technol, Dept Cent Res Inst, Shenzhen 518129, Peoples R China
3.Huawei Cloud Comp Technol Co Ltd, Lab Hlth Intelligence, Guizhou 550025, Peoples R China
4.Huawei Cloud Comp Technol Co Ltd, Lab Hlth Intelligence, Shenzhen 550025, Guizhou, Peoples R China
5.Southern Univ Sci & Technol, Lab Hlth Intelligence, Shenzhen 518055, Peoples R China
6.Int Quantum Acad, Shenzhen 518048, Peoples R China
7.Southern Univ Sci & Technol, Guangdong Prov Key Lab Quantum Sci & Engn, Shenzhen 518055, Peoples R China
8.Southern Univ Sci & Technol, Shenzhen Key Lab Quantum Sci & Engn, Shenzhen 518055, Peoples R China

Li, Yunting,Cui, Xiaopeng,Xiong, Zhaoping,et al. Efficient molecular conformation generation with quantum-inspired algorithm[J]. JOURNAL OF MOLECULAR MODELING,2024,30(7).

Li, Yunting.,Cui, Xiaopeng.,Xiong, Zhaoping.,Zou, Zuoheng.,Liu, Bowen.,...&Yung, Man-Hong.(2024).Efficient molecular conformation generation with quantum-inspired algorithm.JOURNAL OF MOLECULAR MODELING,30(7).

Li, Yunting,et al."Efficient molecular conformation generation with quantum-inspired algorithm".JOURNAL OF MOLECULAR MODELING 30.7(2024).