John Z. H. Zhang

According to our database, John Z. H. Zhang authored at least 47 papers between 2003 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

"Blade of Polarized Water Molecule" Is the Key to Hydrolase Catalysis Regulation.

Yinghui Feng, Yalong Cong, Yue Zhao, Chuanxi Zhang, Hucheng Song, Bohuan Fang, Furong Yang, Huitu Zhang, John Z. H. Zhang, Lujia Zhang

J. Chem. Inf. Model., 2024

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 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

CoRR, 2024

Revolutionizing GPCR-ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery.

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

Briefings Bioinform., 2024

Development and experimental validation of computational methods for human antibody affinity enhancement.

Junxin Li, Linbu Liao, Chao Zhang, Kaifang Huang, Pengfei Zhang, John Z. H. Zhang, Xiaochun Wan, Haiping Zhang

Briefings Bioinform., 2024

2023

Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host-Guest Systems.

Xiao Liu, Lei Zheng, Chu Qin, Yang Li, John Z. H. Zhang, Zhaoxi Sun

J. Chem. Inf. Model., November, 2023

Combined Antibodies Evusheld against the SARS-CoV-2 Omicron Variants BA.1.1 and BA.5: Immune Escape Mechanism from Molecular Simulation.

Jianwen Zhang, Yalong Cong, Lili Duan, John Z. H. Zhang

J. Chem. Inf. Model., August, 2023

MolTaut: A Tool for the Rapid Generation of Favorable Tautomer in Aqueous Solution.

Xiaolin Pan, Fanyu Zhao, Yueqing Zhang, Xingyu Wang, Xudong Xiao, John Z. H. Zhang, Changge Ji

J. Chem. Inf. Model., April, 2023

Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening.

Haiping Zhang, Konda Mani Saravanan, Yanjie Wei, Yang Jiao, Yang Yang, Yi Pan, Xuli Wu, John Z. H. Zhang

J. Chem. Inf. Model., February, 2023

2022

HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models.

Xudong Zhang, Jun Mao, Min Wei, Yifei Qi, John Z. H. Zhang

J. Chem. Inf. Model., 2022

AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking.

Xiaolin Pan, Hao Wang, Yueqing Zhang, Xingyu Wang, Cuiyu Li, Changge Ji, John Z. H. Zhang

J. Chem. Inf. Model., 2022

HobPre: accurate prediction of human oral bioavailability for small molecules.

Min Wei, Xudong Zhang, Xiaolin Pan, Bo Wang, Changge Ji, Yifei Qi, John Z. H. Zhang

J. Cheminformatics, 2022

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure.

Xiao Liu, Lei Zheng, Chu Qin, John Z. H. Zhang, Zhaoxi Sun

J. Comput. Aided Mol. Des., 2022

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant.

Xiao Liu, Lei Zheng, Yalong Cong, Zhihao Gong, Zhixiang Yin, John Z. H. Zhang, Zhirong Liu, Zhaoxi Sun

J. Comput. Aided Mol. Des., 2022

Generating and screening <i>de novo</i> compounds against given targets using ultrafast deep learning models as core components.

Haiping Zhang, Konda Mani Saravanan, Yang Yang, Yanjie Wei, Yi Pan, John Z. H. Zhang

Briefings Bioinform., 2022

2021

Automated Construction of Neural Network Potential Energy Surface: The Enhanced Self-Organizing Incremental Neural Network Deep Potential Method.

Mingyuan Xu, Tong Zhu, John Z. H. Zhang

J. Chem. Inf. Model., 2021

MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network.

Xiaolin Pan, Hao Wang, Cuiyu Li, John Z. H. Zhang, Changge Ji

J. Chem. Inf. Model., 2021

Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis.

Yalong Cong, Yinghui Feng, Hui Ni, Fengdong Zhi, Yulu Miao, Bohuan Fang, Lujia Zhang, John Z. H. Zhang

J. Chem. Inf. Model., 2021

DeepBSP - a Machine Learning Method for Accurate Prediction of Protein-Ligand Docking Structures.

Jingxiao Bao, Xiao He, John Z. H. Zhang

J. Chem. Inf. Model., 2021

2020

DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet.

Yifei Qi, John Z. H. Zhang

J. Chem. Inf. Model., 2020

Development of a New Scoring Function for Virtual Screening: APBScore.

Jingxiao Bao, Xiao He, John Z. H. Zhang

J. Chem. Inf. Model., 2020

Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes.

Zhenliang Wu, Yuwei Zhang, John Z. H. Zhang, Kelin Xia, Fei Xia

J. Comput. Chem., 2020

2019

Accurate and Efficient Calculation of Protein-Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants.

Xiao Liu, Long Peng, John Z. H. Zhang

J. Chem. Inf. Model., 2019

Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning.

Liping He, Jingxiao Bao, Yunpeng Yang, Suzhen Dong, Lujia Zhang, Yifei Qi, John Z. H. Zhang

J. Chem. Inf. Model., 2019

DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks.

Huali Cao, Jingxue Wang, Liping He, Yifei Qi, John Z. H. Zhang

J. Chem. Inf. Model., 2019

BAR-based optimum adaptive steered MD for configurational sampling.

Xiaohui Wang, Xingzhao Tu, Boming Deng, John Z. H. Zhang, Zhaoxi Sun

J. Comput. Chem., 2019

Calculation of hot spots for protein-protein interaction in p53/PMI-MDM2/MDMX complexes.

Dading Huang, Yifei Qi, Jianing Song, John Z. H. Zhang

J. Comput. Chem., 2019

Neural Network Based in Silico Simulation of Combustion Reactions.

Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu, John Z. H. Zhang

CoRR, 2019

2018

Electrostatic Polarization Effect on Cooperative Aggregation of Full Length Human Islet Amyloid.

Yang Li, Xianwei Wang, Longlong Ren, Xuecheng Cao, Changge Ji, Fei Xia, John Z. H. Zhang

J. Chem. Inf. Model., 2018

2017

Protein-Ligand Empirical Interaction Components for Virtual Screening.

Yuna Yan, Weijun Wang, Zhaoxi Sun, John Z. H. Zhang, Changge Ji

J. Chem. Inf. Model., August, 2017

Interaction Entropy for Computational Alanine Scanning.

Yuna Yan, Maoyou Yang, Chang G. Ji, John Z. H. Zhang

J. Chem. Inf. Model., 2017

Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins.

Ya Gao, Chaomin Zhang, John Z. H. Zhang, Ye Mei

J. Chem. Inf. Model., 2017

2016

A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with <i>Candida antarctica</i> Lipase B.

Zhiqiang Yao, Lujia Zhang, Bei Gao, Dongbing Cui, Fengqing Wang, Xiao He, John Z. H. Zhang, Dongzhi Wei

J. Chem. Inf. Model., 2016

PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity.

Xiao Liu, Jinfeng Liu, Tong Zhu, Lujia Zhang, Xiao He, John Z. H. Zhang

J. Chem. Inf. Model., 2016

A new algorithm for construction of coarse-grained sites of large biomolecules.

Min Li, John Z. H. Zhang, Fei Xia

J. Comput. Chem., 2016

2015

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.

Jianzhong Chen, Xingyu Wang, Tong Zhu, Qinggang Zhang, John Z. H. Zhang

J. Chem. Inf. Model., 2015

2014

Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis.

Xiangyu Jia, Juan Zeng, John Z. H. Zhang, Ye Mei

J. Comput. Chem., 2014

2013

Improving the Scoring of Protein-Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization.

Jinfeng Liu, Xiao He, John Z. H. Zhang

J. Chem. Inf. Model., 2013

The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect.

Juan Zeng, Xiangyu Jia, John Z. H. Zhang, Ye Mei

J. Comput. Chem., 2013

A numerically stable restrained electrostatic potential charge fitting method.

Juan Zeng, LiLi Duan, John Z. H. Zhang, Ye Mei

J. Comput. Chem., 2013

Molecular dynamics study of DNA binding by INT-DBD under a polarized force field.

Xue X. Yao, Chang G. Ji, Dai Q. Xie, John Z. H. Zhang

J. Comput. Chem., 2013

2012

Electrostatic polarization is critical for the strong binding in streptavidin-biotin system.

Ye Mei, Yong L. Li, Juan Zeng, John Z. H. Zhang

J. Comput. Chem., 2012

Effect of interprotein polarization on protein-protein binding energy.

Chang G. Ji, John Z. H. Zhang

J. Comput. Chem., 2012

2010

Class I Phospho-inositide-3-kinases (PI3Ks) Isoform-Specific Inhibition Study by the Combination of Docking and Molecular Dynamics Simulation.

Ming Han, John Z. H. Zhang

J. Chem. Inf. Model., 2010

2009

Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions.

Li-Ping Ju, Ke-Li Han, John Z. H. Zhang

J. Comput. Chem., 2009

2008

Efficient bond function basis set for pi-pi interaction energies.

Yun Ding, Ye Mei, John Z. H. Zhang, Fu-Ming Tao

J. Comput. Chem., 2008

2004

Fully quantum mechanical energy optimization for protein-ligand structure.

Yun Xiang, Da W. Zhang, John Z. H. Zhang

J. Comput. Chem., 2004

2003

Molecular caps for full quantum mechanical computation of peptide-water interaction energy.

Da W. Zhang, X. H. Chen, John Z. H. Zhang

J. Comput. Chem., 2003