2026
AutoLoop is an autoregressive deep learning method for protein loop prediction with high accuracy
Tianyue Wang, Xujun Zhang, Langcheng Wang, Odin Zhang, Jike Wang, Ercheng Wang, Jialu Wu, Renling Hu, Jingxuan Ge, Shimeng Li, others
Cell Reports Physical Science, 2026, 7 (1).
Mechanistic Insights into Nitrogenase-Catalyzed Nitrogen Fixation: A QM/MM Study
Jiabin Yin, Jianqiang Feng, Zhenjia Gan, Bowen Li, Binju Wang, Tong Zhu, John ZH Zhang
ACS Catalysis, 2026.
Enhancing the Simulation Accuracy of Small Organic Molecules with an Optimized Lennard-Jones Coarse-Grained Model
Renjie Zhu, Tong Zhu, Ruibo Wu, Fei Xia
2026.
SOT-RM: An equivariant shortcut and optimal transportation-based flow model for exploring chemical reaction mechanisms
Mingyuan Xu, Bowen Li, Zhaojia Dong, Pavlo O Dral, Tong Zhu, Hongming Chen
2026.
A practical framework for rapid calculation of protein polarization energies with anisotropic atomic polarizabilities
Wan-sheng Ren, Jin Xiao, Yingfeng Zhang, Tong Zhu, John ZH Zhang
The Journal of Chemical Physics, 2026, 164 (5).
Understanding the Adsorption and Desorption Dynamics for On-surface Systems
Jin-En He, Mingjun Yang, Zhe-Ning Chen, Tong Zhu, Jun Chen
2026.
2025
Machine Learning Driven ReaxFF Optimization for Combustion
Yueqian Sun, Shuwen Zhang, John ZH Zhang, Tong Zhu
Chinese Journal of Chemical Physics, 2025.
Insights into Binding Mechanisms of Potential Inhibitors Targeting PCSK9 Protein via Molecular Dynamics Simulation and Free Energy Calculation
Xingyu Wu, Xi Zhu, Min Fang, Fenghua Qi, Zhixiang Yin, John ZH Zhang, Shihua Luo, Tong Zhu, Ya Gao
Molecules, 2025, 30 (14), 2962.
Identification of Nogo-B as a potential therapeutic target of osteosarcoma via stereochemically selective covalent probes
Jian Xue, Meng Li, Li Kang, Meiting Wang, Jiabin Yin, Donghui Sun, Yaqi Deng, Qinghua Wei, Jiemin Wong, Tong Zhu, others
Cell Death \& Disease, 2025, 16 (1), 537.
DeePaTB: A deep learning powerd semi-empirical quantum mechanical method
Jin Xiao, Yingfeng Zhang, Bowen Li, Jinzhe Zeng, John ZH Zhang, Tong Zhu
2025.
Deep Learning for Bidirectional Translation between Molecular Structures and Vibrational Spectra
Tianqing Hu, Zihan Zou, Bo Li, Tong Zhu, Shaonan Gu, Jun Jiang, Yi Luo, Wei Hu
Journal of the American Chemical Society, 2025, 147 (31), 27525–27536.
Coarse-Grained Simulation of Persistence Length and Twisting Dynamics of Micrometer-Scale Microtubules
Renjie Zhu, Yuwei Zhang, Tong Zhu, Fei Xia
The Journal of Physical Chemistry Letters, 2025, 16 (29), 7300–7306.
Thiazolidinones as Potential PGK1 Inhibitors for Treatment of Osteosarcoma Growth and Metastasis
Xuwen Chen, Meng Li, Zongjing Hu, Donghui Sun, Yikai Xu, Wenwen Dong, Tong Zhu, Weibin Zhang, Shunying Liu
Journal of Medicinal Chemistry, 2025, 68 (21), 22216–22245.
QM/MM study of cytochrome P450 TxtE catalysis: Substrate reorganization enables selective aromatic nitration
Jiabin Yin, Jianqiang Feng, Zhenjia Gan, Bowen Li, Binju Wang, Lujia Zhang, Tong Zhu, John ZH Zhang
The Journal of Chemical Physics, 2025, 163 (16).
Application of Modern Intelligent Algorithms in Retrosynthesis Prediction
Jianhan Liao, Xiaoxin Shi, Ya Gao, Xingyu Wang, Tong Zhu
Communications in Computational Chemistry, 2025, 7 (4), 289–310.
Time-resolved fluorescent proteins expand fluorescent microscopy in temporal and spectral domains
Zizhu Tan, Chia-Heng Hsiung, Jiahui Feng, Yangye Zhang, Yihan Wan, Junlin Chen, Ke Sun, Peilong Lu, Jianyang Zang, Wenxing Yang, others
Cell, 2025, 188 (24), 6987–7005.
Bohrium+ SciMaster: Building the Infrastructure and Ecosystem for Agentic Science at Scale
Linfeng Zhang, Siheng Chen, Yuzhu Cai, Jingyi Chai, Junhan Chang, Kun Chen, Zhi X Chen, Zhaohan Ding, Yuwen Du, Yuanpeng Gao, others
arXiv preprint arXiv:2512.20469, 2025.
General reactive machine learning potentials for CHON elements
Bowen Li, Sixuan Mi, Jin Xiao, Duo Zhang, Shuwen Zhang, John Zhang, Han Wang, Tong Zhu
2025.
Pretrained E (3)-equivariant message-passing neural networks with multi-level representations for organic molecule spectra prediction
Yuzhi Xu, Daqian Bian, Cheng-Wei Ju, Fanyu Zhao, Pujun Xie, Yuanqing Wang, Wei Hu, Zhenrong Sun, John ZH Zhang, Tong Zhu
npj Computational Materials, 2025, 11 (1), 203.
ECTS: An ultra-fast diffusion model for exploring chemical reactions with equivariant consistency
Mingyuan Xu, Bowen Li, Zhaojia Dong, Pavlo Dral, Tong Zhu, Hongming Chen
2025.
Transition state searching accelerated by neural network potential
Bowen Li, Jin Xiao, Ya Gao, John ZH Zhang, Tong Zhu
Journal of Chemical Information and Modeling, 2025, 65 (5), 2297–2303.
Vib2Mol: from vibrational spectra to molecular structures-a versatile deep learning model
Xinyu Lu, Hao Ma, Hui Li, Jia Li, Tong Zhu, Guokun Liu, Bin Ren
arXiv e-prints, 2025, arXiv–2503.
A graph neural network for the era of large atomistic models
Duo Zhang, Anyang Peng, Chun Cai, Wentao Li, Yuanchang Zhou, Jinzhe Zeng, Mingyu Guo, Chengqian Zhang, Bowen Li, Hong Jiang, others
arXiv preprint arXiv:2506.01686, 2025.
Atmospheric sulfate aerosol formation enhanced by interfacial anions
Gehui Wang, Si Zhang, Can Wu, Tong Zhu, Xinbei Xu, Shuangshuang Ge, Haitao Sun, Zhenrong Sun, Jiaxin Wang, Yuemeng Ji, others
PNAS nexus, 2025, 4 (3), pgaf058.
Real-fluid transport property computations based on the Boltzmann-weighted full-dimensional potential model
Xin Zhang, Junfeng Bai, Bowen Liu, Tong Zhu, Hao Zhao
Applications in Energy and Combustion Science, 2025, 23, 100342.
Ab initio accuracy neural network potential for drug-like molecules
Manyi Yang, Duo Zhang, Xinyan Wang, BoWen Li, Linfeng Zhang, Weinan E, Tong Zhu, Han Wang
Research, 2025, 8, 0837.
The Atomic Density-Based Tight-Binding (aTB) Model: A Robust and Accurate Semiempirical Method Parametrized for H--Ra; Applied to Structures, Vibrational Frequencies, Noncovalent Interactions, and Excited States
Yingfeng Zhang, Jin Xiao, Shunyu Wang, Tong Zhu, John ZH Zhang
Journal of Chemical Theory and Computation, 2025, 21 (7), 3410–3425.
A Deep Learning-Augmented Density Functional Framework for Reaction Modeling with Chemical Accuracy
Jin Xiao, Yingfeng Zhang, Bowen Li, Shuwen Zhang, Ya Gao, Wei Chen, Han Wang, John ZH Zhang, Tong Zhu
JACS Au, 2025, 5 (8), 3892–3903.
2024
A machine learning-based high-precision density functional method for drug-like molecules
Jin Xiao, YiXiao Chen, LinFeng Zhang, Han Wang, Tong Zhu
Artificial Intelligence Chemistry, 2024, 2 (1), 100037.
Designer cellular spheroids with DNA origami for drug screening
Jiayi Wei, Yueyang Sun, Heming Wang, Tong Zhu, Li Li, Ying Zhou, Quan Liu, Zhen Dai, Wenjuan Li, Taihua Yang, others
Science Advances, 2024, 10 (29), eado9880.
Predicting Two-Photon Absorption Spectra of Octupolar Molecules: A Deep-Learning Approach Based Exclusively on Molecular Structures
Haoqing Fu, Mengna Zhang, Jiancai Leng, Wei Hu, Tong Zhu, Yujin Zhang
The Journal of Physical Chemistry A, 2024, 128 (2), 431–438.
Visible-light-promoted $\alpha$-C (sp3)--H amination of ethers with azoles and amides
Yaqi Deng, Zongjing Hu, Jian Xue, Jiabin Yin, Tong Zhu, Shunying Liu
Organic Letters, 2024, 26 (4), 933–938.
Predicting DNA Reactions with a Quantum Chemistry-Based Deep Learning Model
Likun Wang, Na Li, Mengyao Cao, Yun Zhu, Xiewei Xiong, Li Li, Tong Zhu, Hao Pei
Advanced Science, 2024, 11 (42), 2409880.
DPA-2: a large atomic model as a multi-task learner
Duo Zhang, Xinzijian Liu, Xiangyu Zhang, Chengqian Zhang, Chun Cai, Hangrui Bi, Yiming Du, Xuejian Qin, Anyang Peng, Jiameng Huang, others
npj computational materials, 2024, 10 (1), 293.
Enzymatic ring contraction for the biosynthesis of sulfur-containing cyclopentachromone
Qiuyue Nie, Chunxiao Sun, Shuai Liu, Qiang Li, Maria Zotova, Tong Zhu, Xue Gao
Journal of the American Chemical Society, 2024, 147 (1), 548–556.
Discovery of New Synthetic Routes of Amino Acids in Prebiotic Chemistry
Xiao-Tian Li, Sixuan Mi, Yuzhi Xu, Bo-Wen Li, Tong Zhu, John ZH Zhang
JACS Au, 2024, 4 (12), 4757–4768.
The Atomic Density-Based Tight-Binding (aTB) Model: A Robust and Accurate Semiempirical Method Parametrized for H--Ra; Applied to Structures, Vibrational Frequencies, Noncovalent Interactions, and Excited States
Yingfeng Zhang, Jin Xiao, Shunyu Wang, Tong Zhu, John ZH Zhang
Journal of Chemical Theory and Computation, 2025, 21 (7), 3410–3425.
DPA-2: Towards a universal large atomic model for molecular and materials simulation
Han Wang, Duo Zhang, Xinzijian Liu, Xiangyu Zhang, Chengqian Zhang, Chun Cai, Hangrui Bi, Yiming Du, Xuejian Qin, Jiameng Huang, others
2024.
A one-pot photocatalytic triazole-based linkerology for PROTACs
Jinhua Liu, Yaqi Deng, Jiabin Yin, Jian Ji, Cong Guan, Xuwen Chen, Xiang Wu, Tong Zhu, Shunying Liu
Cell Reports Physical Science, 2024, 5 (8).
Iodide ion-enabled highly regioselective $\alpha$-C (sp 3)--H triazolization of ethers with N-sulfonyl-1, 2, 3-triazoles
Yaqi Deng, Jiabin Yin, Zongjing Hu, Jian Xue, Jian Ji, Tong Zhu, Shunying Liu
New Journal of Chemistry, 2024, 48 (34), 15002–15007.
Rapid identification of drug mechanisms with deep learning-based multichannel surface-enhanced Raman spectroscopy
Jiajia Sun, Wei Lai, Jiayan Zhao, Jinhong Xue, Tong Zhu, Mingshu Xiao, Tiantian Man, Ying Wan, Hao Pei, Li Li
ACS sensors, 2024, 9 (8), 4227–4235.
Correction to ``Rapid Identification of Drug Mechanisms with Deep Learning-Based Multichannel Surface-Enhanced Raman Spectroscopy''
Jiajia Sun, Wei Lai, Jiayan Zhao, Jinhong Xue, Tong Zhu, Mingshu Xiao, Tiantian Man, Ying Wan, Hao Pei, Li Li
ACS sensors, 2024, 10 (1), 574–574.
Novel Alkynylamide-Based Nonpeptidic Allosteric Inhibitors for SARS-CoV-2 3-Chymotrypsin-like Protease
Jian Xue, Hongtao Li, Ruyu Wang, Meiting Wang, Xixiang Chen, Yaqi Deng, Jiani Lu, Yexi Li, Yuheng Song, Jianrong Xu, others
ACS Pharmacology \& Translational Science, 2024, 7 (10), 3170–3191.
Discovery of chalcone derivatives as bifunctional molecules with anti-SARS-CoV-2 and anti-inflammatory activities
Xuwen Chen, Hongtao Li, Meiting Wang, Donghui Sun, Jiani Lu, Tong Zhu, Hongzhuan Chen, Lili Chen, Shunying Liu
Journal of Natural Products, 2024, 87 (12), 2680–2694.
On the design space between molecular mechanics and machine learning force fields
Yuanqing Wang, Kenichiro Takaba, Michael S Chen, Marcus Wieder, Yuzhi Xu, Tong Zhu, John ZH Zhang, Arnav Nagle, Kuang Yu, Xinyan Wang, others
Applied Physics Reviews, 2025, 12 (2).
Transition State Searching Accelerated by Deep Learning Potential
Bowen Li, Jin Xiao, Ya Gao, John Zhang, Tong Zhu
2024.
2023
Neural network potentials
Jinzhe Zeng, Liqun Cao, Tong Zhu
Quantum Chemistry in the Age of Machine Learning, 2023, 279–294.
Ensemble-based virtual screening of human PI4KIII$\alpha$ inhibitors toward the Hepatitis C virus
Chen Wang, Ya Gao, Jiaying Gu, Huimin Chen, Zhixiang Yin, Hao Zhu, Tong Zhu
Chemical Physics Letters, 2023, 815, 140354.
Interaction of divalent cations and amino acids in bulk water: Molecular simulations with neural network potentials
Qi Zhang, Tong Zhu
Chinese Journal of Chemical Physics, 2023, 36 (2), 162–168.
Theoretical study of the absorption and emission spectrum and non-adiabatic excited state dynamics of gas-phase xanthone
Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang
Journal of the Chinese Chemical Society, 2023, 70 (3), 372–385.
Regioselectively Electrochemical Synthesis of N 2-Selective C--H Amination of Ethers with N-Tosyl 1, 2, 3-Triazole via Triazole Radical Cation
Cong Guan, Jiabin Yin, Jian Ji, Jinhua Liu, Xiang Wu, Tong Zhu, Shunying Liu
Organic Letters, 2023, 25 (28), 5383–5388.
Function-oriented synthesis of Imidazo [1, 2-a] pyrazine and Imidazo [1, 2-b] pyridazine derivatives as potent PI3K/mTOR dual inhibitors
Chuchu Li, Yuqiao Han, Zhengyang Wang, Yanan Yu, Chen Wang, Ziwei Ren, Yanzhi Guo, Tong Zhu, XuWen Li, Suzhen Dong, others
European Journal of Medicinal Chemistry, 2023, 247, 115030.
A new inhibitor of human peptide deformylase suppresses cell proliferation and induces cell apoptosis and autophagy in cancers
Yanzhi Guo, Yuqiao Han, Ziyan Li, Jiali Ji, Tong Zhu, Yijie Du, Suzhen Dong
Anti-Cancer Drugs, 2023, 34 (4), 483–494.
DPA-2: Towards a universal large atomic model for molecular and material simulation
Duo Zhang, Xinzijian Liu, Xiangyu Zhang, Chengqian Zhang, Chun Cai, Hangrui Bi, Yiming Du, Xuejian Qin, Jiameng Huang, Bowen Li, others
arXiv e-prints, 2023, arXiv–2312.
Theoretical investigation of the lack of chiral self-sorting behaviour of a molecular cinquefoil knot
Xinyi Zhao, Raorao Yang, Zhi-Hui Zhang, Tong Zhu, Liang Zhang
Supramolecular Chemistry, 2023, 34 (5-6), 247–256.
Front Cover: Enzyme-Free Nucleic Acid Circuits for Fold-Change Detection (ChemPlusChem 9/2023).
Likun Wang, Jiayan Zhao, Xiewei Xiong, Li Li, Tong Zhu, Hao Pei
ChemPlusChem, 2023, 88 (9).
Enzyme-Free Nucleic Acid Circuits for Fold-Change Detection
Likun Wang, Jiayan Zhao, Xiewei Xiong, Li Li, Tong Zhu, Hao Pei
ChemPlusChem, 2023, 88 (9), e202300083.
A Machine Learning Protocol to Directly Translate Molecular Infrared or Raman Spectra into Molecular Formula
Wei Hu, Tianqing Hu, Bo Li, Zihan Zou, Tong Zhu, Yujin Zhang, Jun Jiang, Yi Luo
2023.
EnviroDetaNet: Pretrained E (3)-equivariant Message-Passing Neural Networks with Multi-Level Molecular Representations for Organic Molecule Spectra Prediction
Yuzhi Xu, Daqian Bian, Cheng-Wei Ju, Fanyu Zhao, Pujun Xie, Yuanqing Wang, Wei Hu, Zhenrong Sun, John Zhang, Tong Zhu
2024.
2022
Exploring the selective mechanism of inhibitors towards different subtypes of class I PI3K
Xiaoniu Fang, Ya Gao, Chen Wang, Huimin Chen, Tong Zhu
Chemical Physics Letters, 2022, 786, 139174.
Theoretical investigations on photodissociation dynamics of deuterated alkyl halides CD3CH2F
Shuangfei Gu, Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang
Chinese Journal of Chemical Physics, 2022, 35 (3), 431–442.
Ab initio neural network MD simulation of thermal decomposition of a high energy material CL-20/TNT
Liqun Cao, Jinzhe Zeng, Bo Wang, Tong Zhu, John ZH Zhang
Physical Chemistry Chemical Physics, 2022, 24 (19), 11801–11811.
An efficient method to predict protein thermostability in alanine mutation
Ya Gao, Bo Wang, Shiyu Hu, Tong Zhu, John ZH Zhang
Physical Chemistry Chemical Physics, 2022, 24 (48), 29629–29639.
Multiplex base-editing enables combinatorial epigenetic regulation for genome mining of fungal natural products
Fanglong Zhao, Chunxiao Sun, Zhiwen Liu, Alan Cabrera, Mario Escobar, Shunyu Huang, Qichen Yuan, Qiuyue Nie, Kevin Lee Luo, Angela Lin, others
Journal of the American Chemical Society, 2022, 145 (1), 413–421.
Molecular convolutional neural networks with DNA regulatory circuits
Xiewei Xiong, Tong Zhu, Yun Zhu, Mengyao Cao, Jin Xiao, Li Li, Fei Wang, Chunhai Fan, Hao Pei
Nature Machine Intelligence, 2022, 4 (7), 625–635.
Growth of polycyclic aromatic hydrocarbon and soot inception by in silico simulation
Bo Wang, Jinzhe Zeng, Liqun Cao, Chih-Hao Chin, Darrin York, Tong Zhu, John Zhang
2022.
Novel 2-phenyl-3-(Pyridin-2-yl) thiazolidin-4-one derivatives as potent inhibitors for proliferation of osteosarcoma cells in vitro and in vivo
Yaqi Deng, Rou Pi, Li Niu, Yun Zhao, Dan Ni, Longlong Song, Zi Li, Wangyujing Han, Qinghua Wei, Yuqiao Han, others
European Journal of Medicinal Chemistry, 2022, 228, 114010.
Design, synthesis, and biological evaluation of imidazo [1, 2-a] pyridine derivatives as novel PI3K/mTOR dual inhibitors
Ya'nan Yu, Yuqiao Han, Fupo Zhang, Zhenmei Gao, Tong Zhu, Suzhen Dong, Mingliang Ma
Journal of Medicinal Chemistry, 2020, 63 (6), 3028–3046.
2021
Automatically Construct Neural Network Potentials for Molecular Dynamics Simulation of Zinc Proteins
Mingyuan Xu, Tong Zhu, John ZH Zhang
Frontiers in Chemistry, 2021, 9, 385.
DOI: 10.3389/fchem.2021.692200
Extensive Evaluation of Force Fields for G-Quadruplexes
Na Li, Tong Zhu
ChemRxiv Preprint.
DOI: 10.26434/chemrxiv.14369897
Binding Mechanisms of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations
Junxiao Chen, Na Li, Xingyu Wang, Jianzhong Chen, John ZH Zhang, Tong Zhu
Physical Chemistry Chemical Physics, 2021.
DOI: 10.1039/D0CP06438F
Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement
Yao Liu, Yalong Cong, Chuanxi Zhang, Bohuan Fang, Yue Pan, Qiangzi Li, Chun You, Bei Gao, John ZH Zhang, Tong Zhu, Lujia Zhang
RSC Advances, 2021, 11 (20), 12036–12042.
DOI: 10.1039/D1RA00352F
Exploring the Chemical Space of Linear Alkane Pyrolysis via Deep Potential GENerator
Jinzhe Zeng, Linfeng Zhang, Han Wang, Tong Zhu
Energy & Fuels, 2021, 35 (1), 762–769.
DOI: 10.1021/acs.energyfuels.0c03211
Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins
Zhiwen Liu, Fanglong Zhao, Boyang Zhao, Jie Yang, Joseph Ferrara, Banumathi Sankaran, BV Venkataram Prasad, Biki Bapi Kundu, George N Phillips Jr, Yang Gao, others
Nature communications, 2021, 12 (1), 4158.
Benchmark force fields for the molecular dynamic simulation of G-quadruplexes
Na Li, Ya Gao, Feng Qiu, Tong Zhu
Molecules, 2021, 26 (17), 5379.
Molecular convolutional neural networks with DNA regulatory circuits
Hao Pei, Xiewei Xiong, Tong Zhu, Yun Zhu, Mengyao Cao, Jin Xiao, Li Li, Fei Wang, Chunhai Fan
2021.
Fragment-based ab initio molecular dynamics simulation for combustion
Liqun Cao, Jinzhe Zeng, Mingyuan Xu, Chih-Hao Chin, Tong Zhu, John ZH Zhang
Molecules, 2021, 26 (11), 3120.
Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: A theoretical study
Chih-Hao Chin, Tong Zhu, John ZH Zhang
Physical Chemistry Chemical Physics, 2021.
DOI: 10.1039/D1CP00133G