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)

Fully quantum mechanical energy optimization for protein-ligand structure. - Yun Xiang; Da W. Zhang; John Z. H. Zhang (J. Comput. Chem., 2004)

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)

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)

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)

Effect of interprotein polarization on protein-protein binding energy. - Chang G. Ji; John Z. H. Zhang (J. Comput. Chem., 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)

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)

A numerically stable restrained electrostatic potential charge fitting method. - Juan Zeng; LiLi Duan; John Z. H. Zhang; Ye Mei (J. Comput. Chem., 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)

Improving the Scoring of Protein-Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization. - Jinfeng Liu 004; Xiao He 004; John Z. H. Zhang (J. Chem. Inf. Model., 2013)

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)

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)

A new algorithm for construction of coarse-grained sites of large biomolecules. - Min Li; John Z. H. Zhang; Fei Xia (J. Comput. Chem., 2016)

PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity. - Xiao Liu; Jinfeng Liu 004; Tong Zhu; Lujia Zhang; Xiao He 004; John Z. H. Zhang (J. Chem. Inf. Model., 2016)

A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with Candida antarctica Lipase B. - Zhiqiang Yao; Lujia Zhang; Bei Gao; Dongbing Cui; Fengqing Wang; Xiao He 004; John Z. H. Zhang; Dongzhi Wei (J. Chem. Inf. Model., 2016)

Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins. - Ya Gao 004; Chaomin Zhang; John Z. H. Zhang; Ye Mei (J. Chem. Inf. Model., 2017)

Interaction Entropy for Computational Alanine Scanning. - Yuna Yan; Maoyou Yang; Chang G. Ji; John Z. H. Zhang (J. Chem. Inf. Model., 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., 2017)

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)

Neural Network Based in Silico Simulation of Combustion Reactions. - Jinzhe Zeng; Liqun Cao; Mingyuan Xu; Tong Zhu; John Z. H. Zhang (CoRR, 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)

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)

DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks. - Huali Cao; Jingxue Wang 003; Liping He; Yifei Qi; 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)

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)

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)

Development of a New Scoring Function for Virtual Screening: APBScore. - Jingxiao Bao; Xiao He 004; John Z. H. Zhang (J. Chem. Inf. Model., 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)

DeepBSP - a Machine Learning Method for Accurate Prediction of Protein-Ligand Docking Structures. - Jingxiao Bao; Xiao He 004; John Z. H. Zhang (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)

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)

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)

Generating and screening de novo compounds against given targets using ultrafast deep learning models as core components. - Haiping Zhang; Konda Mani Saravanan; Yang Yang; Yanjie Wei; Yi Pan 001; John Z. H. Zhang (Briefings Bioinform., 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)

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)

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)

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)

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)

Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening. - Haiping Zhang; Konda Mani Saravanan; Yanjie Wei; Yang Jiao; Yang Yang; Yi Pan 001; Xuli Wu; John Z. H. Zhang (J. Chem. Inf. Model., 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., 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., 2023)

Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host-Guest Systems. - Xiao Liu; Lei Zheng; Chu Qin; Yang Li 123; John Z. H. Zhang; Zhaoxi Sun (J. Chem. Inf. Model., 2023)

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)

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)

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; et al. (CoRR, 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)

ChemXTree: A Feature-Enhanced Graph Neural Network-Neural Decision Tree Framework for ADMET Prediction. - Yuzhi Xu; Xinxin Liu; Wei Xia; Jiankai Ge; Cheng-Wei Ju; Haiping Zhang; John Z. H. Zhang (J. Chem. Inf. Model., 2024)

Significantly enhancing human antibody affinity via deep learning and computational biology-guided single-point mutations. - 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 (Briefings Bioinform., 2025)

Transition State Searching Accelerated by Neural Network Potential. - Bowen Li; Jin Xiao; Ya Gao; John Z. H. Zhang; Tong Zhu (J. Chem. Inf. Model., 2025)