John Zenghui Zhang

Director, NYU-ECNU Center for Computational Chemistry at NYU Shanghai
Professor of Chemistry, NYU; Global Network Professor, NYU Shanghai

Email: john.zhang@nyu.edu

John Zenghui Zhang received his B.S. degree from the Physics Department of East China Normal University in 1982 and his Ph.D. degree from University of Houston in 1987. He did his postdoctoral research at UC Berkeley from 1987 to 1990. He was an Assistant Professor of Chemistry at NYU from 1990-1994, an Associate Professor from 1994-1997, and has been a Professor since 1997.

Professor Zhang’s current research focus is the development and application of novel computational methods for accurate and efficient study of biological systems. He develops quantum and classical methods, including new polarized force field, to accurately predict protein structure, free energy in protein-drug and protein-protein bindings, conformational dynamics of membrane proteins, structure and dynamics of metalloproteins. John Zhang has received many prestigious awards, including the Camille and Henry Dreyfus New Faculty Award (1990), the NSF Presidential Faculty Fellow (1994), the Alfred P. Sloan Foundation Research Fellow (1995) and the Camille Dreyfus Teacher-Scholar (1995).

 

Recent Publications:

  • Yinghui Feng, Xiaomei Lyu, Yalong Cong, Tingwei Miao, Bohuan Fang, Chuanxi Zhang, Qiang Shen, Melissa Matthews, Andrew J. Fisher, John Z.H. Zhang, Lujia Zhang* , Ruijin Yang*, A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction, International Journal of Biological Macromolecules, 2023, 253, 127093.
  • Xianwei Wang,* Yiying Wang, Man Guo, Xuechao Wang, Yang Li,* and John Z.H. Zhang*, Assessment of an Electrostatic Energy-Based Charge Model for Modeling the Electrostatic Interactions in Water Solvent, Journal Of Chemical Theory And Computation, 2023, 19, 6294−6312.
  • Mengxin Li, Yalong Cong, Yifei Qi* and John Z. H. Zhang*, Binding of berberine derivates to G-quadruplex: insight from a computational study, Physical Chemistry Chemical Physics, 2023, 25, 10741.
  • Jianwen Zhang, Yalong Cong, Lili Duan,* and 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, Journal of Chemical Information and Modeling, 2023, 63, 5297−5308.
  • Xiao Liu*, Lei Zheng, Chu Qin, Yalong Cong* , John Z. H. Zhang and Zhaoxi Sun*, Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host–Guest Binding: III. ForceField Comparison, Three-Trajectory Realization and Further Dielectric Augmentation, Molecules, 2023, 28, 2767.
  • Haiping Zhang,* Konda Mani Saravanan, Yanjie Wei, Yang Jiao, Yang Yang, Yi Pan, Xuli Wu, and John Z. H. Zhang*, Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening, Journal of Chemical Information and Modeling, 2023, 63, 835−845.
  • Haiping Zhang* , Konda Mani Saravanan, and John Z. H. Zhang*, DeepBindGCN: Integrating Molecular Vector Representation with Graph Convolutional Neural Networks for Protein–Ligand Interaction Prediction, Molecules, 2023, 28, 4691.
  • Chuang Li, Aiwei Zhang, Lifei Wang, Jiaqi Zuo, Caizhen Zhu, Jian Xu, Mingliang Wang*, John Z.H. Zhang*, Development of a polynomial scoring function P3-Score for improved scoring and ranking powers, Chemical Physics Letters, 2023, 824, 140547.
  • Lili Duan,Bolin Tang,Song Luo,Danyang Xiong,Qihang Wang,Xiaole Xu,John Z. H. Zhang,Entropy driven cooperativity efect in multi‑site drug optimization targeting SARS‑CoV‑2 papain‑like protease, Cellular and Molecular Life Sciences, 2023, 80, 313.
  • Xiaolin Pan, Fanyu Zhao, Yueqing Zhang, Xingyu Wang, Xudong Xiao, John Z. H. Zhang and Changge Ji, MolTaut: A Tool for the Rapid Generation of Favorable Tautomer in Aqueous Solution, Journal of Chemical Information and Modeling, 2023, 63, 1833−1840.
  • Mingzhe Ma, Yalong Cong, John Z. H. Zhang, Lujia Zhang, Rational Design of a Highly Specific Prolyl Endopeptidase To Activate the Antihypertensive Effect of Peptides, ChemBioChem, 2023, 24, e202200691.
  • Mingzhe Ma, Yinghui Feng, Yulu Miao, Qiang Shen, Shuting Tang, Juan Dong, John Z. H. Zhang, Lujia Zhang, Revealing the Sequence Characteristics and Molecular Mechanisms of ACE Inhibitory Peptides by Comprehensive Characterization of 160,000 Tetrapeptides, Foods, 2023, 12, 1573.
  • Xiao Liu, Lei Zheng, Chu Qin, Yang Li, John Z. H. Zhang, and Zhaoxi Sun, Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host−Guest Systems, Journal of Chemical Information and Modeling, 2023, 63, 6938−6946.
  • Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang, Theoretical study of the absorption and emission spectrum and non-adiabatic excited state dynamics of gas-phase xanthone, Journal of the Chinese Chemical Society, 2023, 70, 372-385.
  • 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, Journal of Computer-Aided Molecular Design, 2022, 36, 879–894.
  • Zhen Li, Haiqing Bai, Xuetong Xi, Wen-xia Tian, John Z.H. Zhang, Demin Zhou, Longlong Si*, PROTAC vaccine: A new way to live attenuated vaccines, Clinical and Translational Medicine, 2022, 12, e1081.
  • 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, Journal of Computer-Aided Molecular Design, 2022, 36, 735–752.
  • Yalong Cong, Mengxin Li, Yifei Qi and John Z. H. Zhang*, A fast-slow method to treat solute dynamics in explicit solvent, Physical Chemistry Chemical Physics, 2022, 24, 14498–14510. 
  • Zhendong Li and John Z. H. Zhang*, Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2, Biomolecules, 2022, 12, 4, 572.
  • Liqun Cao, Jinzhe Zeng, Bo Wang, Tong Zhu* and John Z. H. Zhang*, Ab initio neural network MD simulation of thermal decomposition of a high energy material CL-20/TNT, Physical Chemistry Chemical Physics, 2022, 24, 11801-11811.
  • Lei Zheng, Yunpeng Yang, Jingxiao Bao, Liping He, Yifei Qi*, John Z. H. Zhang*, Discovery of novel inhibitors of CDK2 using docking and physics-based binding free energy calculation, Chemical Biology & Drug Design, 2022, 99, 662–673.
  • Min Wei, Xudong Zhang, Xiaolin Pan, Bo Wang, Changge Ji, Yifei Qi* and John Z. H. Zhang*, HobPre: accurate prediction of human oral bioavailability for small molecules, Journal of Cheminformatics, 2022, 14, 1. 
  • Xudong Zhang, Jun Mao, Min Wei, Yifei Qi,* and John Z. H. Zhang*, HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models, J. Chem. Inf. Model., 2022, 62, 1830−1839.
  • Yue Pan, Jinxiao Bao, Xingyi Zhang, Hui Ni, Yue Zhao, Fengdong Zhi, Bohuan Fang, Xiao He*, John Z. H. Zhang* and Lujia Zhang*, Rational Design of P450 aMOx for Improving Anti-Markovnikov Selectivity Based on the “Butterfly” Model, Frontiers in Molecular Biosciences, 2022, 9, 888721.
  • Haiping Zhang* , Konda Mani Saravanan, Yang Yang, Yanjie Wei , Pan Yi and John Z.H. Zhang*, Generating and screening de novo compounds against given targets using ultrafast deep learning models as core components, Briefings in Bioinformatics, 2022, 23(4), 1–15.
  • Danyang Xiong, Xiaoyu Zhao, Song Luo, John Z. H. Zhang*, and Lili Duan*, Molecular Mechanism of the Non-Covalent Orally Targeted SARSCoV‑2 Mpro Inhibitor S‑217622 and Computational Assessment of Its Effectiveness against Mainstream Variants, J. Phys. Chem. Lett., 2022, 13, 8893−8901.
  • Haiping Zhang*, Xiaohua Gong, Yun Peng, Konda Mani Saravanan, Hengwei Bian, John Z. H. Zhang, Yanjie Wei, Yi Pan and Yang Yang*, An Efficient Modern Strategy to Screen Drug Candidates Targeting RdRp of SARS-CoV-2 With Potentially High Selectivity and Specificity, Frontiers in Chemistry, 2022, 10, 933102.
  • Bo Wang, Jun Mao, Min Wei, Yifei Qi* and John Z. H. Zhang*, SeBPPI: A Sequence-Based Protein-Protein Binding Predictor, J. Comput. Biophys. Chem., 2022, 21(6), 729–737.
  • Yue Zhao, Yulu Miao, Yalong Cong, Jiawei Wang, Fengdong Zhi, Yue Pan, Jianguo Zhang, John Z.H. Zhang*, Lujia Zhang* , High-level expression and improved pepsin activity by enhancing the conserved domain stability based on a scissor-like model, LWT-Food Science and Technology, 2022, 167, 113877.
  • Danyang Xiong, Xiaoyu Zhao, Song Luo, Yalong Cong, John Z. H. Zhang,* and Lili Duan*, Immune Escape Mechanisms of SARS-CoV‑2 Delta and Omicron Variants against Two Monoclonal Antibodies That Received Emergency Use Authorization. J. Phys. Chem. Letts. 2022, 13, 6064−6073.
  • Shuangfei Gu, Chih-Hao Chin*, Tong Zhu*, and John Zeng Hui Zhang, Theoretical investigations on photodissociation dynamics of deuterated alkyl halides CD3CH2F, Chinese Journal of Chemical Physics, 2022, 35, 431,
  • Xiaolin Pan, Hao Wang, Yueqing Zhang, Xingyu Wang, Cuiyu Li, Changge Ji,* and John Z. H. Zhang*, AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking, J. Chem. Inf. Model., 2022, 62, 2499−2509.