John Z. H. Zhang

50 papers Journal 50
YearRankTypeTitle / Venue / Authors
2025 J jnl
Significantly enhancing human antibody affinity via deep learning and computational biology-guided single-point mutations.
Briefings Bioinform.
Junxin Li, Chao Zhang, Wei Xia, Hei Wun Kan, Kaifang Huang, Sai Li, Mark Akinola Ige, Qiuliyang Yu, Jiawei Zhao, Xiaochun Wan, John Z. H. Zhang, Haiping Zhang
2025 J jnl
Transition State Searching Accelerated by Neural Network Potential.
J. Chem. Inf. Model.
Bowen Li, Jin Xiao, Ya Gao, John Z. H. Zhang, Tong Zhu
2024 J jnl
"Blade of Polarized Water Molecule" Is the Key to Hydrolase Catalysis Regulation.
J. Chem. Inf. Model.
Yinghui Feng, Yalong Cong, Yue Zhao, Chuanxi Zhang, Hucheng Song, Bohuan Fang, Furong Yang, Huitu Zhang, John Z. H. Zhang, Lujia Zhang
2024 J jnl
ChemXTree: A Feature-Enhanced Graph Neural Network-Neural Decision Tree Framework for ADMET Prediction.
J. Chem. Inf. Model.
Yuzhi Xu, Xinxin Liu, Wei Xia, Jiankai Ge, Cheng-Wei Ju, Haiping Zhang, John Z. H. Zhang
2024 J jnl
Development and experimental validation of computational methods for human antibody affinity enhancement.
Briefings Bioinform.
Junxin Li, Linbu Liao, Chao Zhang, Kaifang Huang, Pengfei Zhang, John Z. H. Zhang, Xiaochun Wan, Haiping Zhang
2024 J jnl
On the design space between molecular mechanics and machine learning force fields.
CoRR
Yuanqing Wang, Kenichiro Takaba, Michael S. Chen, Marcus Wieder, Yuzhi Xu, Tong Zhu, John Z. H. Zhang, Arnav Nagle, Kuang Yu, Xinyan Wang, Daniel J. Cole, Joshua A. Rackers, Kyunghyun Cho, Joe G. Greener, Peter K. Eastman, Stefano Martiniani, Mark E. Tuckerman
2024 J jnl
Revolutionizing GPCR-ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery.
Briefings Bioinform.
Haiping Zhang, Hongjie Fan, Jixia Wang, Tao Hou, Konda Mani Saravanan, Wei Xia, Hei Wun Kan, Junxin Li, John Z. H. Zhang, Xinmiao Liang, Yang Chen
2023 J jnl
Combined Antibodies Evusheld against the SARS-CoV-2 Omicron Variants BA.1.1 and BA.5: Immune Escape Mechanism from Molecular Simulation.
J. Chem. Inf. Model.
Jianwen Zhang, Yalong Cong, Lili Duan, John Z. H. Zhang
2023 J jnl
Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening.
J. Chem. Inf. Model.
Haiping Zhang, Konda Mani Saravanan, Yanjie Wei, Yang Jiao, Yang Yang, Yi Pan, Xuli Wu, John Z. H. Zhang
2023 J jnl
MolTaut: A Tool for the Rapid Generation of Favorable Tautomer in Aqueous Solution.
J. Chem. Inf. Model.
Xiaolin Pan, Fanyu Zhao, Yueqing Zhang, Xingyu Wang, Xudong Xiao, John Z. H. Zhang, Changge Ji
2023 J jnl
Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host-Guest Systems.
J. Chem. Inf. Model.
Xiao Liu, Lei Zheng, Chu Qin, Yang Li, John Z. H. Zhang, Zhaoxi Sun
2022 J jnl
AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking.
J. Chem. Inf. Model.
Xiaolin Pan, Hao Wang, Yueqing Zhang, Xingyu Wang, Cuiyu Li, Changge Ji, John Z. H. Zhang
2022 J jnl
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure.
J. Comput. Aided Mol. Des.
Xiao Liu, Lei Zheng, Chu Qin, John Z. H. Zhang, Zhaoxi Sun
2022 J jnl
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant.
J. Comput. Aided Mol. Des.
Xiao Liu, Lei Zheng, Yalong Cong, Zhihao Gong, Zhixiang Yin, John Z. H. Zhang, Zhirong Liu, Zhaoxi Sun
2022 J jnl
Generating and screening
Briefings Bioinform.
Haiping Zhang, Konda Mani Saravanan, Yang Yang, Yanjie Wei, Yi Pan, John Z. H. Zhang
2022 J jnl
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models.
J. Chem. Inf. Model.
Xudong Zhang, Jun Mao, Min Wei, Yifei Qi, John Z. H. Zhang
2022 J jnl
HobPre: accurate prediction of human oral bioavailability for small molecules.
J. Cheminformatics
Min Wei, Xudong Zhang, Xiaolin Pan, Bo Wang, Changge Ji, Yifei Qi, John Z. H. Zhang
2021 J jnl
Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis.
J. Chem. Inf. Model.
Yalong Cong, Yinghui Feng, Hui Ni, Fengdong Zhi, Yulu Miao, Bohuan Fang, Lujia Zhang, John Z. H. Zhang
2021 J jnl
Automated Construction of Neural Network Potential Energy Surface: The Enhanced Self-Organizing Incremental Neural Network Deep Potential Method.
J. Chem. Inf. Model.
Mingyuan Xu, Tong Zhu, John Z. H. Zhang
2021 J jnl
DeepBSP - a Machine Learning Method for Accurate Prediction of Protein-Ligand Docking Structures.
J. Chem. Inf. Model.
Jingxiao Bao, Xiao He, John Z. H. Zhang
2021 J jnl
MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network.
J. Chem. Inf. Model.
Xiaolin Pan, Hao Wang, Cuiyu Li, John Z. H. Zhang, Changge Ji
2020 J jnl
DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet.
J. Chem. Inf. Model.
Yifei Qi, John Z. H. Zhang
2020 J jnl
Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes.
J. Comput. Chem.
Zhenliang Wu, Yuwei Zhang, John Z. H. Zhang, Kelin Xia, Fei Xia
2020 J jnl
Development of a New Scoring Function for Virtual Screening: APBScore.
J. Chem. Inf. Model.
Jingxiao Bao, Xiao He, John Z. H. Zhang
2019 J jnl
Accurate and Efficient Calculation of Protein-Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants.
J. Chem. Inf. Model.
Xiao Liu, Long Peng, John Z. H. Zhang
2019 J jnl
BAR-based optimum adaptive steered MD for configurational sampling.
J. Comput. Chem.
Xiaohui Wang, Xingzhao Tu, Boming Deng, John Z. H. Zhang, Zhaoxi Sun
2019 J jnl
Calculation of hot spots for protein-protein interaction in p53/PMI-MDM2/MDMX complexes.
J. Comput. Chem.
Dading Huang, Yifei Qi, Jianing Song, John Z. H. Zhang
2019 J jnl
DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks.
J. Chem. Inf. Model.
Huali Cao, Jingxue Wang, Liping He, Yifei Qi, John Z. H. Zhang
2019 J jnl
Neural Network Based in Silico Simulation of Combustion Reactions.
CoRR
Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu, John Z. H. Zhang
2019 J jnl
Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning.
J. Chem. Inf. Model.
Liping He, Jingxiao Bao, Yunpeng Yang, Suzhen Dong, Lujia Zhang, Yifei Qi, John Z. H. Zhang
2018 J jnl
Electrostatic Polarization Effect on Cooperative Aggregation of Full Length Human Islet Amyloid.
J. Chem. Inf. Model.
Yang Li, Xianwei Wang, Longlong Ren, Xuecheng Cao, Changge Ji, Fei Xia, John Z. H. Zhang
2017 J jnl
Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins.
J. Chem. Inf. Model.
Ya Gao, Chaomin Zhang, John Z. H. Zhang, Ye Mei
2017 J jnl
Interaction Entropy for Computational Alanine Scanning.
J. Chem. Inf. Model.
Yuna Yan, Maoyou Yang, Chang G. Ji, John Z. H. Zhang
2017 J jnl
Protein-Ligand Empirical Interaction Components for Virtual Screening.
J. Chem. Inf. Model.
Yuna Yan, Weijun Wang, Zhaoxi Sun, John Z. H. Zhang, Changge Ji
2016 J jnl
A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with
J. Chem. Inf. Model.
Zhiqiang Yao, Lujia Zhang, Bei Gao, Dongbing Cui, Fengqing Wang, Xiao He, John Z. H. Zhang, Dongzhi Wei
2016 J jnl
A new algorithm for construction of coarse-grained sites of large biomolecules.
J. Comput. Chem.
Min Li, John Z. H. Zhang, Fei Xia
2016 J jnl
PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity.
J. Chem. Inf. Model.
Xiao Liu, Jinfeng Liu, Tong Zhu, Lujia Zhang, Xiao He, John Z. H. Zhang
2015 J jnl
A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods.
J. Chem. Inf. Model.
Jianzhong Chen, Xingyu Wang, Tong Zhu, Qinggang Zhang, John Z. H. Zhang
2014 J jnl
Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis.
J. Comput. Chem.
Xiangyu Jia, Juan Zeng, John Z. H. Zhang, Ye Mei
2013 J jnl
A numerically stable restrained electrostatic potential charge fitting method.
J. Comput. Chem.
Juan Zeng, Lili Duan, John Z. H. Zhang, Ye Mei
2013 J jnl
Improving the Scoring of Protein-Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization.
J. Chem. Inf. Model.
Jinfeng Liu, Xiao He, John Z. H. Zhang
2013 J jnl
Molecular dynamics study of DNA binding by INT-DBD under a polarized force field.
J. Comput. Chem.
Xue X. Yao, Chang G. Ji, Dai Q. Xie, John Z. H. Zhang
2013 J jnl
The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect.
J. Comput. Chem.
Juan Zeng, Xiangyu Jia, John Z. H. Zhang, Ye Mei
2012 J jnl
Effect of interprotein polarization on protein-protein binding energy.
J. Comput. Chem.
Chang G. Ji, John Z. H. Zhang
2012 J jnl
Electrostatic polarization is critical for the strong binding in streptavidin-biotin system.
J. Comput. Chem.
Ye Mei, Yong L. Li, Juan Zeng, John Z. H. Zhang
2010 J jnl
Class I Phospho-inositide-3-kinases (PI3Ks) Isoform-Specific Inhibition Study by the Combination of Docking and Molecular Dynamics Simulation.
J. Chem. Inf. Model.
Ming Han, John Z. H. Zhang
2009 J jnl
Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions.
J. Comput. Chem.
Li-Ping Ju, Ke-Li Han, John Z. H. Zhang
2008 J jnl
Efficient bond function basis set for pi-pi interaction energies.
J. Comput. Chem.
Yun Ding, Ye Mei, John Z. H. Zhang, Fu-Ming Tao
2004 J jnl
Fully quantum mechanical energy optimization for protein-ligand structure.
J. Comput. Chem.
Yun Xiang, Da W. Zhang, John Z. H. Zhang
2003 J jnl
Molecular caps for full quantum mechanical computation of peptide-water interaction energy.
J. Comput. Chem.
Da W. Zhang, X. H. Chen, John Z. H. Zhang