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Zha J, Su J, Li T, Cao C, Ma Y, Wei H, Huang Z, Qian L, Wen K, Zhang J. Encoding Molecular Docking for Quantum Computers. J Chem Theory Comput 2023; 19:9018-9024. [PMID: 38090816 DOI: 10.1021/acs.jctc.3c00943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Molecular docking is important in drug discovery but is burdensome for classical computers. Here, we introduce Grid Point Matching (GPM) and Feature Atom Matching (FAM) to accelerate pose sampling in molecular docking by encoding the problem into quadratic unconstrained binary optimization (QUBO) models so that it could be solved by quantum computers like the coherent Ising machine (CIM). As a result, GPM shows a sampling power close to that of Glide SP, a method performing an extensive search. Moreover, it is estimated to be 1000 times faster on the CIM than on classical computers. Our methods could boost virtual drug screening of small molecules and peptides in future.
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Affiliation(s)
- Jinyin Zha
- Beijing QBoson Quantum Technology Co., Ltd., Beijing 100015, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiaqi Su
- Beijing QBoson Quantum Technology Co., Ltd., Beijing 100015, China
| | - Tiange Li
- Beijing QBoson Quantum Technology Co., Ltd., Beijing 100015, China
| | - Chongyu Cao
- Beijing QBoson Quantum Technology Co., Ltd., Beijing 100015, China
| | - Yin Ma
- Beijing QBoson Quantum Technology Co., Ltd., Beijing 100015, China
| | - Hai Wei
- Beijing QBoson Quantum Technology Co., Ltd., Beijing 100015, China
| | - Zhiguo Huang
- China Mobile (Suzhou) Software Technology Company Limited, Suzhou 215163, China
| | - Ling Qian
- China Mobile (Suzhou) Software Technology Company Limited, Suzhou 215163, China
| | - Kai Wen
- Beijing QBoson Quantum Technology Co., Ltd., Beijing 100015, China
| | - Jian Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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