John Z. H. Zhang

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 31

Top Topics

Scoring Function

Comprehensive Evaluation

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

Briefings Bioinform.

J. Comput. Aided Mol. Des.

Publications

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
Revolutionizing GPCR-ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery. Briefings Bioinform. 25 (4) (2024)
Jianwen Zhang, Yalong Cong, Lili Duan, John Z. H. Zhang
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. 63 (16) (2023)
Haiping Zhang, Konda Mani Saravanan, Yanjie Wei, Yang Jiao, Yang Yang, Yi Pan, Xuli Wu, John Z. H. Zhang
Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening. J. Chem. Inf. Model. 63 (3) (2023)
Xiaolin Pan, Fanyu Zhao, Yueqing Zhang, Xingyu Wang, Xudong Xiao, John Z. H. Zhang, Changge Ji
MolTaut: A Tool for the Rapid Generation of Favorable Tautomer in Aqueous Solution. J. Chem. Inf. Model. 63 (7) (2023)
Xiao Liu, Lei Zheng, Chu Qin, Yang Li, John Z. H. Zhang, Zhaoxi Sun
Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host-Guest Systems. J. Chem. Inf. Model. 63 (21) (2023)
Xudong Zhang, Jun Mao, Min Wei, Yifei Qi, John Z. H. Zhang
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models. J. Chem. Inf. Model. 62 (8) (2022)
Xiao Liu, Lei Zheng, Yalong Cong, Zhihao Gong, Zhixiang Yin, John Z. H. Zhang, Zhirong Liu, Zhaoxi Sun
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. 36 (12) (2022)
Xiao Liu, Lei Zheng, Chu Qin, John Z. H. Zhang, Zhaoxi Sun
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure. J. Comput. Aided Mol. Des. 36 (10) (2022)
Haiping Zhang, Konda Mani Saravanan, Yang Yang, Yanjie Wei, Yi Pan, John Z. H. Zhang
compounds against given targets using ultrafast deep learning models as core components. Briefings Bioinform. 23 (4) (2022)
Xiaolin Pan, Hao Wang, Yueqing Zhang, Xingyu Wang, Cuiyu Li, Changge Ji, John Z. H. Zhang
AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking. J. Chem. Inf. Model. 62 (10) (2022)
Min Wei, Xudong Zhang, Xiaolin Pan, Bo Wang, Changge Ji, Yifei Qi, John Z. H. Zhang
HobPre: accurate prediction of human oral bioavailability for small molecules. J. Cheminformatics 14 (1) (2022)
Jingxiao Bao, Xiao He, John Z. H. Zhang
DeepBSP - a Machine Learning Method for Accurate Prediction of Protein-Ligand Docking Structures. J. Chem. Inf. Model. 61 (5) (2021)
Xiaolin Pan, Hao Wang, Cuiyu Li, John Z. H. Zhang, Changge Ji
MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network. J. Chem. Inf. Model. 61 (7) (2021)
Mingyuan Xu, Tong Zhu, John Z. H. Zhang
Automated Construction of Neural Network Potential Energy Surface: The Enhanced Self-Organizing Incremental Neural Network Deep Potential Method. J. Chem. Inf. Model. 61 (11) (2021)
Yalong Cong, Yinghui Feng, Hui Ni, Fengdong Zhi, Yulu Miao, Bohuan Fang, Lujia Zhang, John Z. H. Zhang
Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis. J. Chem. Inf. Model. 61 (7) (2021)
Zhenliang Wu, Yuwei Zhang, John Z. H. Zhang, Kelin Xia, Fei Xia
Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes. J. Comput. Chem. 41 (1) (2020)
Yifei Qi, John Z. H. Zhang
DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet. J. Chem. Inf. Model. 60 (3) (2020)
Jingxiao Bao, Xiao He, John Z. H. Zhang
Development of a New Scoring Function for Virtual Screening: APBScore. J. Chem. Inf. Model. 60 (12) (2020)
Xiaohui Wang, Xingzhao Tu, Boming Deng, John Z. H. Zhang, Zhaoxi Sun
BAR-based optimum adaptive steered MD for configurational sampling. J. Comput. Chem. 40 (12) (2019)
Liping He, Jingxiao Bao, Yunpeng Yang, Suzhen Dong, Lujia Zhang, Yifei Qi, John Z. H. Zhang
Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning. J. Chem. Inf. Model. 59 (9) (2019)
Dading Huang, Yifei Qi, Jianing Song, John Z. H. Zhang
Calculation of hot spots for protein-protein interaction in p53/PMI-MDM2/MDMX complexes. J. Comput. Chem. 40 (9) (2019)
Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu, John Z. H. Zhang
Neural Network Based in Silico Simulation of Combustion Reactions. CoRR (2019)
Xiao Liu, Long Peng, John Z. H. Zhang
Accurate and Efficient Calculation of Protein-Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants. J. Chem. Inf. Model. 59 (1) (2019)
Huali Cao, Jingxue Wang, Liping He, Yifei Qi, John Z. H. Zhang
DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks. J. Chem. Inf. Model. 59 (4) (2019)
Yang Li, Xianwei Wang, Longlong Ren, Xuecheng Cao, Changge Ji, Fei Xia, John Z. H. Zhang
Electrostatic Polarization Effect on Cooperative Aggregation of Full Length Human Islet Amyloid. J. Chem. Inf. Model. 58 (8) (2018)
Ya Gao, Chaomin Zhang, John Z. H. Zhang, Ye Mei
Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins. J. Chem. Inf. Model. 57 (2) (2017)
Yuna Yan, Maoyou Yang, Chang G. Ji, John Z. H. Zhang
Interaction Entropy for Computational Alanine Scanning. J. Chem. Inf. Model. 57 (5) (2017)
Yuna Yan, Weijun Wang, Zhaoxi Sun, John Z. H. Zhang, Changge Ji
Protein-Ligand Empirical Interaction Components for Virtual Screening. J. Chem. Inf. Model. 57 (8) (2017)
Xiao Liu, Jinfeng Liu, Tong Zhu, Lujia Zhang, Xiao He, John Z. H. Zhang
PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity. J. Chem. Inf. Model. 56 (5) (2016)
Zhiqiang Yao, Lujia Zhang, Bei Gao, Dongbing Cui, Fengqing Wang, Xiao He, John Z. H. Zhang, Dongzhi Wei
Lipase B. J. Chem. Inf. Model. 56 (10) (2016)
Min Li, John Z. H. Zhang, Fei Xia
A new algorithm for construction of coarse-grained sites of large biomolecules. J. Comput. Chem. 37 (9) (2016)
Jianzhong Chen, Xingyu Wang, Tong Zhu, Qinggang Zhang, John Z. H. Zhang
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. 55 (9) (2015)
Xiangyu Jia, Juan Zeng, John Z. H. Zhang, Ye Mei
Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis. J. Comput. Chem. 35 (9) (2014)
Jinfeng Liu, Xiao He, John Z. H. Zhang
Improving the Scoring of Protein-Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization. J. Chem. Inf. Model. 53 (6) (2013)
Juan Zeng, LiLi Duan, John Z. H. Zhang, Ye Mei
A numerically stable restrained electrostatic potential charge fitting method. J. Comput. Chem. 34 (10) (2013)
Xue X. Yao, Chang G. Ji, Dai Q. Xie, John Z. H. Zhang
Molecular dynamics study of DNA binding by INT-DBD under a polarized force field. J. Comput. Chem. 34 (13) (2013)
Juan Zeng, Xiangyu Jia, John Z. H. Zhang, Ye Mei
The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect. J. Comput. Chem. 34 (31) (2013)
Chang G. Ji, John Z. H. Zhang
Effect of interprotein polarization on protein-protein binding energy. J. Comput. Chem. 33 (16) (2012)
Ye Mei, Yong L. Li, Juan Zeng, John Z. H. Zhang
Electrostatic polarization is critical for the strong binding in streptavidin-biotin system. J. Comput. Chem. 33 (15) (2012)
Ming Han, John Z. H. Zhang
Class I Phospho-inositide-3-kinases (PI3Ks) Isoform-Specific Inhibition Study by the Combination of Docking and Molecular Dynamics Simulation. J. Chem. Inf. Model. 50 (1) (2010)
Li-Ping Ju, Ke-Li Han, John Z. H. Zhang
Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions. J. Comput. Chem. 30 (2) (2009)
Yun Ding, Ye Mei, John Z. H. Zhang, Fu-Ming Tao
Efficient bond function basis set for pi-pi interaction energies. J. Comput. Chem. 29 (2) (2008)
Yun Xiang, Da W. Zhang, John Z. H. Zhang
Fully quantum mechanical energy optimization for protein-ligand structure. J. Comput. Chem. 25 (12) (2004)
Da W. Zhang, X. H. Chen, John Z. H. Zhang
Molecular caps for full quantum mechanical computation of peptide-water interaction energy. J. Comput. Chem. 24 (15) (2003)