John Zenghui Zhang (John Z H Zhang, John Z Zhang)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 66

Top Topics

High Temperature

Top Venues

Journal of chemical information and modeling

Molecules (Basel, Switzerland)

Physical chemistry chemical physics : PCCP

Journal of chemical theory and computation

This page only lists publications with an associated author ORCID identifier.

Publications

Mengchen Zhou, Fanyu Zhao, Lan Yu, Jinfeng Liu, Jian Wang, John Zenghui Zhang
An Efficient Approach to the Accurate Prediction of Mutational Effects in Antigen Binding to the MHC1. Molecules (Basel, Switzerland) 29 (4) (2024)
Liujiang Dai, Pengfei Yu, Hongjie Fan, Wei Xia, Yaopeng Zhao, Pengfei Zhang, John Zenghui Zhang, Haiping Zhang, Yang Chen
Identification and Validation of New DNA-PKcs Inhibitors through High-Throughput Virtual Screening and Experimental Verification. International journal of molecular sciences 25 (14) (2024)
Liujiang Dai, Pengfei Yu, Hongjie Fan, Wei Xia, Yaopeng Zhao, Pengfei Zhang, John Zenghui Zhang, Haiping Zhang, Yang Chen
Identification and Validation of New DNA-PKcs Inhibitors through High-Throughput Virtual Screening and Experimental Verification. International journal of molecular sciences 25 (14) (2024)
Wenhao Gu, John Zenghui Zhang
Substituent effects on the selectivity of ambimodal [6+4]/[4+2] cycloaddition. Physical chemistry chemical physics : PCCP 26 (12) (2024)
Mengchen Zhou, Fanyu Zhao, Lan Yu, Jinfeng Liu, Jian Wang, John Zenghui Zhang
An Efficient Approach to the Accurate Prediction of Mutational Effects in Antigen Binding to the MHC1. Molecules (Basel, Switzerland) 29 (4) (2024)
Liujiang Dai, Pengfei Yu, Hongjie Fan, Wei Xia, Yaopeng Zhao, Pengfei Zhang, John Zenghui Zhang, Haiping Zhang, Yang Chen
Identification and Validation of New DNA-PKcs Inhibitors through High-Throughput Virtual Screening and Experimental Verification. International journal of molecular sciences 25 (14) (2024)
Mengchen Zhou, Fanyu Zhao, Lan Yu, Jinfeng Liu, Jian Wang, John Zenghui Zhang
An Efficient Approach to the Accurate Prediction of Mutational Effects in Antigen Binding to the MHC1. Molecules (Basel, Switzerland) 29 (4) (2024)
Wenhao Gu, John Zenghui Zhang
Substituent effects on the selectivity of ambimodal [6+4]/[4+2] cycloaddition. Physical chemistry chemical physics : PCCP (2024)
Xiao Liu, Lei Zheng, Chu Qin, Yang Li, John Zenghui Zhang, Zhaoxi Sun
Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host-Guest Systems. Journal of chemical information and modeling (2023)
Xian-Wei Wang, Yiying Wang, Man Guo, Xuechao Wang, Yang Li, John Zenghui Zhang
Assessment of an Electrostatic Energy-Based Charge Model for Modeling the Electrostatic Interactions in Water Solvent. Journal of chemical theory and computation (2023)
Xiao Liu, Lei Zheng, Chu Qin, Yalong Cong, John Zenghui Zhang, Zhaoxi Sun
Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation. Molecules (Basel, Switzerland) 28 (6) (2023)
Mingzhe Ma, Yinghui Feng, Yulu Miao, Qiang Shen, Shuting Tang, Juan Dong, John Zenghui Zhang, Lujia Zhang
Revealing the Sequence Characteristics and Molecular Mechanisms of ACE Inhibitory Peptides by Comprehensive Characterization of 160,000 Tetrapeptides. Foods (Basel, Switzerland) 12 (8) (2023)
Mengxin Li, Yalong Cong, Yifei Qi, John Zenghui Zhang
Binding of berberine derivates to G-quadruplex: insight from a computational study. Physical chemistry chemical physics : PCCP (2023)
Jianwen Zhang, Yalong Cong, Lili Duan, John Zenghui Zhang
Combined Antibodies Evusheld against the SARS-CoV-2 Omicron Variants BA.1.1 and BA.5: Immune Escape Mechanism from Molecular Simulation. Journal of chemical information and modeling (2023)
Mingzhe Ma, Yinghui Feng, Yulu Miao, Qiang Shen, Shuting Tang, Juan Dong, John Zenghui Zhang, Lujia Zhang
Revealing the Sequence Characteristics and Molecular Mechanisms of ACE Inhibitory Peptides by Comprehensive Characterization of 160,000 Tetrapeptides. Foods (Basel, Switzerland) 12 (8) (2023)
Xiaolin Pan, Fanyu Zhao, Yueqing Zhang, Xingyu Wang, Xudong Xiao, John Zenghui Zhang, Changge Ji
MolTaut: A Tool for the Rapid Generation of Favorable Tautomer in Aqueous Solution. Journal of chemical information and modeling (2023)
Xiao Liu, Lei Zheng, Chu Qin, Yalong Cong, John Zenghui Zhang, Zhaoxi Sun
Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation. Molecules (Basel, Switzerland) 28 (6) (2023)
Xiao Liu, Lei Zheng, Chu Qin, Yalong Cong, John Zenghui Zhang, Zhaoxi Sun
Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation. Molecules (Basel, Switzerland) 28 (6) (2023)
Yongtao Xu, Baoyi Fan, Yunlong Gao, Yifan Chen, Di Han, Jiarui Lu, Taigang Liu, Qinghe Gao, John Zenghui Zhang, Meiting Wang
Design Two Novel Tetrahydroquinoline Derivatives against Anticancer Target LSD1 with 3D-QSAR Model and Molecular Simulation. Molecules (Basel, Switzerland) 27 (23) (2022)
Danyang Xiong, Xiaoyu Zhao, Song Luo, Yalong Cong, John Zenghui Zhang, Lili Duan
Immune Escape Mechanisms of SARS-CoV-2 Delta and Omicron Variants against Two Monoclonal Antibodies That Received Emergency Use Authorization. The journal of physical chemistry letters 13 (26) (2022)
Yongtao Xu, Baoyi Fan, Yunlong Gao, Yifan Chen, Di Han, Jiarui Lu, Taigang Liu, Qinghe Gao, John Zenghui Zhang, Meiting Wang
Design Two Novel Tetrahydroquinoline Derivatives against Anticancer Target LSD1 with 3D-QSAR Model and Molecular Simulation. Molecules (Basel, Switzerland) 27 (23) (2022)
Danyang Xiong, Xiaoyu Zhao, Song Luo, John Zenghui Zhang, Lili Duan
Molecular Mechanism of the Non-Covalent Orally Targeted SARS-CoV-2 M pro Inhibitor S-217622 and Computational Assessment of Its Effectiveness against Mainstream Variants. The journal of physical chemistry letters 13 (38) (2022)
Liqun Cao, Jinzhe Zeng, Bo Wang, Tong Zhu, John Zenghui Zhang
Ab initio neural network MD simulation of thermal decomposition of a high energy material CL-20/TNT. Physical chemistry chemical physics : PCCP 24 (19) (2022)
Longlong Ren, Zhenxiang Jing, Fei Xia, John Zenghui Zhang, Yang Li
Toxic Effect of Fullerene and Its Derivatives upon the Transmembrane β 2 -Adrenergic Receptors. Molecules (Basel, Switzerland) 27 (14) (2022)
Xudong Zhang, Jun Mao, Min Wei, John Z H Zhang, John Zenghui Zhang
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models. Journal of chemical information and modeling 62 (8) (2022)
Yongtao Xu, Baoyi Fan, Yunlong Gao, Yifan Chen, Di Han, Jiarui Lu, Taigang Liu, Qinghe Gao, John Zenghui Zhang, Meiting Wang
Design Two Novel Tetrahydroquinoline Derivatives against Anticancer Target LSD1 with 3D-QSAR Model and Molecular Simulation. Molecules (Basel, Switzerland) 27 (23) (2022)
Yongtao Xu, Baoyi Fan, Yunlong Gao, Yifan Chen, Di Han, Jiarui Lu, Taigang Liu, Qinghe Gao, John Zenghui Zhang, Meiting Wang
Design Two Novel Tetrahydroquinoline Derivatives against Anticancer Target LSD1 with 3D-QSAR Model and Molecular Simulation. Molecules (Basel, Switzerland) 27 (23) (2022)
Zhendong Li, John Zenghui Zhang
Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2. Biomolecules 12 (4) (2022)
Xiaolin Pan, Hao Wang, Yueqing Zhang, Xingyu Wang, Cuiyu Li, Changge Ji, John Zenghui Zhang
AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking. Journal of chemical information and modeling 62 (10) (2022)
Mingyuan Xu, Tong Zhu, John Zenghui Zhang
Automated Construction of Neural Network Potential Energy Surface: The Enhanced Self-Organizing Incremental Neural Network Deep Potential Method. Journal of chemical information and modeling 61 (11) (2021)
Jingxiao Bao, Xiao He, John Zenghui Zhang
DeepBSP-a Machine Learning Method for Accurate Prediction of Protein-Ligand Docking Structures. Journal of chemical information and modeling 61 (5) (2021)
Xian-Wei Wang, Xilong Li, Xiao He, John Zenghui Zhang
A fixed multi-site interaction charge model for an accurate prediction of the QM/MM interactions. Physical chemistry chemical physics : PCCP 23 (37) (2021)
Xian-Wei Wang, Jinhua Yan, Hang Zhang, Zhousu Xu, John Zenghui Zhang
An electrostatic energy-based charge model for molecular dynamics simulation. The Journal of chemical physics 154 (13) (2021)
Xiaolin Pan, Hao Wang, Cuiyu Li, John Zenghui Zhang, Changge Ji
MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network. Journal of chemical information and modeling 61 (7) (2021)
Yalong Cong, Yinghui Feng, Hui Ni, Fengdong Zhi, Yulu Miao, Bohuan Fang, Lujia Zhang, John Zenghui Zhang
Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis. Journal of chemical information and modeling 61 (7) (2021)
Yuwei Zhang, Zexing Cao, John Zenghui Zhang, Fei Xia
Double-Well Ultra-Coarse-Grained Model to Describe Protein Conformational Transitions. Journal of chemical theory and computation 16 (10) (2020)
Bo Wang, Cuiyu Li, Jia Xiangyu, Tong Zhu, John Zenghui Zhang
An Approach to Computing Solvent Reorganization Energy. Journal of chemical theory and computation 16 (10) (2020)
Dading Huang, Shuaizhen Tian, Yifei Qi, John Zenghui Zhang
Binding Modes of Small-Molecule Inhibitors to the EED Pocket of PRC2. Chemphyschem : a European journal of chemical physics and physical chemistry 21 (3) (2020)
Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu, John Zenghui Zhang
Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation. Nature communications 11 (1) (2020)
Fengyu Li, John Zenghui Zhang, Fei Xia
How CuCl and CuCl2 Insert into C-N Bonds of Diazo Compounds: An Electronic Structure and Mechanistic Study. The journal of physical chemistry. A 124 (10) (2020)
Xiaolin Li, Yalong Cong, Mingzhe Ma, Zhi-Neng You, Bei Gao, John Zenghui Zhang, Lujia Zhang
An Energy Optimization Strategy Based on the Perfect Conformation of Prolyl Endopeptidase for Improving Catalytic Efficiency. Journal of agricultural and food chemistry 68 (18) (2020)
Jingxiao Bao, Xiao He, John Zenghui Zhang
Development of a New Scoring Function for Virtual Screening: APBScore. Journal of chemical information and modeling 60 (12) (2020)
John Z H Zhang, John Zenghui Zhang
DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet. Journal of chemical information and modeling 60 (3) (2020)
Jianzhong Chen, Laixue Pang, Wei Wang, Lifei Wang, John Zenghui Zhang, Tong Zhu
Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations. Journal of biomolecular structure & dynamics 38 (4) (2019)
Zhenliang Wu, Yuwei Zhang, John Zenghui Zhang, Kelin Xia, Fei Xia
Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes. Journal of computational chemistry 41 (1) (2019)
Xiaohui Wang, Xingzhao Tu, Boming Deng, John Zenghui Zhang, Zhaoxi Sun
BAR-based optimum adaptive steered MD for configurational sampling. Journal of computational chemistry 40 (12) (2019)
Mingyuan Xu, Xiao He, Tong Zhu, John Zenghui Zhang
A Fragment Quantum Mechanical Method for Metalloproteins. Journal of chemical theory and computation 15 (2) (2019)
Zhengrong Xiao, Yalong Cong, Kaifang Huang, Susu Zhong, John Zenghui Zhang, Lili Duan
Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy. Physical chemistry chemical physics : PCCP 21 (37) (2019)
Jianzhong Chen, Baohua Yin, Laixue Pang, Wei Wang, John Zenghui Zhang, Tong Zhu
Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies. Journal of biomolecular structure & dynamics 38 (7) (2019)
Ercheng Wang, Huiyong Sun, Junmei Wang, Zhe Wang, Hui Liu, John Zenghui Zhang, Ting-Jun Hou
End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chemical reviews 119 (16) (2019)
Mingyuan Xu, Tong Zhu, John Zenghui Zhang
Molecular Dynamics Simulation of Zinc Ion in Water with an ab Initio Based Neural Network Potential. The journal of physical chemistry. A 123 (30) (2019)
Zhaoxi Sun, Xiaohui Wang, John Zenghui Zhang
Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR-ligand binding. Physical chemistry chemical physics : PCCP 22 (3) (2019)
Dading Huang, Wei Wen, Xiao Liu, Yang Li, John Zenghui Zhang
Computational analysis of hot spots and binding mechanism in the PD-1/PD-L1 interaction. RSC advances 9 (26) (2019)
Liping He, Jingxiao Bao, Yunpeng Yang, Suzhen Dong, Lujia Zhang, John Z H Zhang, John Zenghui Zhang
Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning. Journal of chemical information and modeling 59 (9) (2019)
Zhaoxi Sun, Xiaohui Wang, John Zenghui Zhang, Qiaole He
Sulfur-substitution-induced base flipping in the DNA duplex. Physical chemistry chemical physics : PCCP 21 (27) (2019)
Huali Cao, Jingxue Wang, Liping He, John Z H Zhang, John Zenghui Zhang
DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks. Journal of chemical information and modeling 59 (4) (2019)
Xiao Liu, Long Peng, John Zenghui Zhang
Accurate and Efficient Calculation of Protein-Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants. Journal of chemical information and modeling 59 (1) (2018)
Dading Huang, Yifei Qi, Jianing Song, John Zenghui Zhang
Calculation of hot spots for protein-protein interaction in p53/PMI-MDM2/MDMX complexes. Journal of computational chemistry 40 (9) (2018)
Jin-Feng Liu, John Zenghui Zhang, Xiao He
Probing the Ion-Specific Effects at the Water/Air Interface and Water-Mediated Ion Pairing in Sodium Halide Solution with Ab Initio Molecular Dynamics. The journal of physical chemistry. B 122 (44) (2018)
Min Li, John Zenghui Zhang
Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins. Physical chemistry chemical physics : PCCP 19 (10) (2018)
Jin-Feng Liu, Jason Swails, John Zenghui Zhang, Xiao He, Adrian E Roitberg
A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease. Journal of the American Chemical Society 140 (5) (2018)
Xiao Liu, Long Peng, Yifan Zhou, Youzhi Zhang, John Zenghui Zhang
Computational Alanine Scanning with Interaction Entropy for Protein-Ligand Binding Free Energies. Journal of chemical theory and computation 14 (3) (2018)
Jinfeng Liu, Lian-Wen Qi, John Zenghui Zhang, Xiao He
Fragment Quantum Mechanical Method for Large-Sized Ion-Water Clusters. Journal of chemical theory and computation 13 (5) (2017)
Yuna Yan, Maoyou Yang, Chang G Ji, John Zenghui Zhang
Interaction Entropy for Computational Alanine Scanning. Journal of chemical information and modeling 57 (5) (2017)
Yuna Yan, Weijun Wang, Zhaoxi Sun, John Zenghui Zhang, Changge Ji
Protein-Ligand Empirical Interaction Components for Virtual Screening. Journal of chemical information and modeling 57 (8) (2017)
Zhoujie Luo, Ya Gao, Tong Zhu, John Zenghui Zhang, Fei Xia
Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules. The journal of physical chemistry. A 121 (34) (2017)