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ORCIDJohn Z. H. Zhang
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2020 – today
- 2024
[j43]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)- [i2]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:
On the design space between molecular mechanics and machine learning force fields. CoRR abs/2409.01931 (2024) - 2023
- [j42]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): 835-845 (2023) - [j41]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): 1833-1840 (2023) - [j40]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): 5297-5308 (2023) - [j39]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): 6938-6946 (2023) - 2022
- [j38]Haiping Zhang, Konda Mani Saravanan, Yang Yang, Yanjie Wei, Yi Pan, John Z. H. Zhang:
Generating and screening de novo compounds against given targets using ultrafast deep learning models as core components. Briefings Bioinform. 23(4) (2022) - [j37]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): 735-752 (2022) - [j36]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): 879-894 (2022) - [j35]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): 1 (2022) - [j34]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): 1830-1839 (2022) - [j33]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): 2499-2509 (2022) - 2021
- [j32]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): 2231-2240 (2021) - [j31]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): 3159-3165 (2021) - [j30]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): 3529-3542 (2021) - [j29]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): 5425-5437 (2021) - 2020
- [j28]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): 14-20 (2020) - [j27]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): 1245-1252 (2020) - [j26]Jingxiao Bao, Xiao He, John Z. H. Zhang:
Development of a New Scoring Function for Virtual Screening: APBScore. J. Chem. Inf. Model. 60(12): 6355-6365 (2020)
2010 – 2019
- 2019
- [j25]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): 1045-1056 (2019) - [j24]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): 1270-1289 (2019) - [j23]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): 272-281 (2019) - [j22]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): 1508-1514 (2019) - [j21]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): 3871-3878 (2019) - [i1]Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu, John Z. H. Zhang:
Neural Network Based in Silico Simulation of Combustion Reactions. CoRR abs/1911.12252 (2019) - 2018
- [j20]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): 1587-1595 (2018) - 2017
- [j19]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): 267-274 (2017) - [j18]Yuna Yan, Maoyou Yang, Chang G. Ji, John Z. H. Zhang:
Interaction Entropy for Computational Alanine Scanning. J. Chem. Inf. Model. 57(5): 1112-1122 (2017) - [j17]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): 1793-1806 (2017) - 2016
- [j16]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): 795-804 (2016) - [j15]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): 854-861 (2016) - [j14]Zhiqiang Yao, Lujia Zhang, Bei Gao, Dongbing Cui, Fengqing Wang, Xiao He, John Z. H. Zhang, Dongzhi Wei:
A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with Candida antarctica Lipase B. J. Chem. Inf. Model. 56(10): 1979-1994 (2016) - 2015
- [j13]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): 1903-1913 (2015) - 2014
- [j12]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): 737-747 (2014) - 2013
- [j11]Juan Zeng, LiLi Duan, John Z. H. Zhang, Ye Mei:
A numerically stable restrained electrostatic potential charge fitting method. J. Comput. Chem. 34(10): 847-853 (2013) - [j10]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): 1136-1142 (2013) - [j9]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): 2677-2686 (2013) - [j8]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): 1306-1314 (2013) - 2012
- [j7]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): 1374-1382 (2012) - [j6]Chang G. Ji, John Z. H. Zhang:
Effect of interprotein polarization on protein-protein binding energy. J. Comput. Chem. 33(16): 1416-1420 (2012) - 2010
- [j5]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): 136-145 (2010)
2000 – 2009
- 2009
- [j4]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): 305-316 (2009) - 2008
- [j3]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): 275-279 (2008) - 2004
- [j2]Yun Xiang, Da W. Zhang, John Z. H. Zhang:
Fully quantum mechanical energy optimization for protein-ligand structure. J. Comput. Chem. 25(12): 1431-1437 (2004) - 2003
- [j1]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): 1846-1852 (2003)
Coauthor Index
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