John Z.H. Zhang

Professor of Chemistry

Education

B.S. East China Normal University

Ph.D. University of Houston

Postdoctoral Research at University of California, Berkeley

Areas of Research/Interest

Computational study of protein’s structure and interaction dynamics.

External Affiliations

Theoretical and Computational Chemistry Committee of Chinese Chemical Society

Chemical Dynamics Committee of Chinese Chemical Society

Protein Committee of Chinese Biochemistry and Molecular Biology Society

Academic Advisory Committee of the State Key Lab of Molecular Reaction Dynamics of the Institute of Chemical Physics of Chinese Academy of Science

Academic Advisory Committee of Key Lab of Computational Material Science of Chinese Ministry of Education

Shanghai Biophysical Society (standing committee member)

Fellowships/Honors

Camille and Henry Dreyfus New Faculty Award (1990)

NSF Presidential Faculty Fellow (1994)

Alfred P. Sloan Foundation Research Fellow (1995)

amille Dreyfus Teacher-Scholar (1995)

Selected Publications

J.F. Liu, J.Z.H. Zhang, X. He, “Probing the Ion-Specific Effects at the Water/Air Interface and Water-Mediated Ion Pairing in Sodium Halide Solution with Ab Initio Molecular Dynamics”, J. Phys. Chem. B, 122, 10202-10209 (2018).

J.F. Liu, X. He, J.Z.H. Zhang, L.W. Qi, “Hydrogen-bond structure dynamics in bulk water: insights from ab initio simulations with coupled cluster theory”, Chem. Sci., 9, 2065-2073 (2018).

Y. Li, X.W. Wang, L.L. Ren, X.C. Cao, C.G. Ji, F. Xia, J.Z.H. Zhang, “Electrostatic Polarization Effect on Cooperative Aggregation of Full Length Human Islet Amyloid”, J. Chem. Inf. Model., 58, 1587-1595 (2018).

Y. Gao, T. Zhu, C.M. Zhang, J.Z.H. Zhang, Y. Mei, “Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations”, Chem. Phys. Lett. 706, 594–600 (2018).

X.H. Wang, X.Z. Tu, J.Z.H. Zhang, Z.X. Sun, “BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification”, Phys. Chem. Chem. Phys., 20, 2009-2021 (2018).

H.Y. Sun, L.L. Duan, F. Chen, H. Liu, Z. Wang, P.C. Pan, F. Zhu, J.Z.H. Zhang, T.J. Hou, “Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches”, Phys. Chem. Chem. Phys., 20, 14450-14460 (2018).

J.N. Song, L.Q. Song, J.Z.H. Zhang, “An efficient method for computing excess free energy of liquid”, Sci. China Chem., 61,135-140 (2018).

X. Liu, L. Peng, J.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., doi: 10.1021/acs.jcim.8b00248 (2018).

Y.F. Zhou, X. Liu, Y.Z. Zhang, L. Peng, J.Z.H. Zhang, “Residue-specific free energy analysis in ligand bindings to JAK2”, Mol. Phys., 116, 2633-2641 (2018).

L.Q. Qiu, C. Shen, J.N. Song, Y.K. Zhang, J.Z.H. Zhang, “Functional loop dynamics of the S-component of ECF transporter FolT”, Mol. Phys., 116, 2613-2621 (2018).

J.F. Liu, J. Swails, J.Z.H. Zhang, X. He, A.E. Roitberg, “A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease”, J. Am. Chem. Soc., 140, 1639-1648 (2018).

X. Liu, L. Peng, Y.F. Zhou, Y.Z. Zhang, J.Z.H. Zhang, “Computational Alanine Scanning with Interaction Entropy for Protein-Ligand Binding Free Energies”, J. Chem. Theory Comput., 14, 1772-1780 (2018).

J.X. Wang, H.L. Cao, J.Z.H. Zhang, Y.F. Qi, “Computational Protein Design with Deep Learning Neural Networks”, Sci. Rep., 8, 6349, (2018).

X.S. Jin, T. Zhu, J.Z.H. Zhang, X. He, “Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes”, Front. Chem., 6, 150, (2018).

M.Y. Xu， T. Zhu, J.Z.H. Zhang, “A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein”, Front. Chem., 6, 189, (2018).

Z.Q. Yao, S.Q. Jiang, L.J. Zhang, B. Gao, X. He, J.Z.H. Zhang, “Crius: A novel fragment-based algorithm of de novo substrate prediction for enzymes”, Protein Sci., 27, 8, 1526-1534 (2018).

Y.L. Cong, Y.C. Li, K. Jin, S.S. Zhong, J.Z.H. Zhang, H. Li, L.L. Duan, “Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field”, Front. Chem., 6, 380, (2018).

L.Q. Qiu, Y.N. Yan, Z.X. Sun, J.N. Song, John Z.H. Zhang, “Interaction entropy for computational alanine scanning in protein–protein binding”, WIREs Comput. Mol. Sci., 8:e1342, doi: 10.1002/wcms.1342 (2018).

Y. Gao, C.M. Zhang, John Z.H. Zhang, and Y. Mei, “Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins”, J. Chem. Inf. Model., 57, 267−274 (2017).

S. Li, A.W. Zhu, T. Zhu, John Z.H. Zhang, and Y. Tian, “Single Biosensor for Simultaneous Quantification of Glucose and pH in a Rat Brain of Diabetic Model Using Both Current and Potential Outputs”, Anal. Chem., 89, 6656−6662 (2017).

L. Liu, F. Zhao, W. Liu, T. Zhu, John Z.H. Zhang, C. Chen, Z.H. Dai, H.S. Peng, J.L. Huang, Q. Hu, W.B. Bu, and Y. Tian, “An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O2 in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy”, Angew. Chem.-Int. Edit., 56, 35, 10471-10475 (2017).

M.M. Huang, Z.J. Luo, T. Zhu, J. Chen, John Z.H. Zhang, F. Xia, “A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquids”, RSC Adv., 7(81), 51521-51527 (2017).

Z.X. Sun, X.H. Wang, John Z.H. Zhang, “Protonation-dependent base flipping in the catalytic triad of a small RNA”, Chem. Phys. Lett., 684, 239-244 (2017).

Z.X. Sun, T. Zhu, X.H. Wang, Y. Mei, John Z.H. Zhang, “Optimization of convergence criteria for fragmentation methods”, Chem. Phys. Lett., 687, 163-170 (2017).

Z.X. Sun, Y.N. Yan, M.Y. Yang, John Z.H. Zhang, “Interaction entropy for protein-protein binding”, J. Chem. Phys., 146, 124124 (2017).

M. Li, John Z.H. Zhang, “Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins”, Phys. Chem. Chem. Phys., 19(10), 7410-7419 (2017).

J.F. Liu, X. He, John Z.H. Zhang, “Structure of liquid water - a dynamical mixture of tetrahedral and 'ring-and-chain' like structures”, Phys. Chem. Chem. Phys., 19(19), 11931-11936 (2017).

Y.N. Yan, W.J. Wang, Z.X. Sun, John Z.H. Zhang, C.G. Ji, “Protein-Ligand Empirical Interaction Components for Virtual Screening”, J. Chem. Inf. Model., 57(8), 1793-1806 (2017).

M. Li, John Z.H. Zhang, “Protein simulation using coarse-grained two-bead multipole force field with polarizable water models”, J. Chem. Phys., 146(6), 065101 (2017).

Y.N. Yan, M.Y. Yang, C.G. Ji, John Z.H. Zhang, “Interaction Entropy for Computational Alanine Scanning”, J. Chem. Inf. Model., 57(5), 1112-1122 (2017).

X.S. Jin, John Z.H. Zhang, X. He, “Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method”, J. Phys. Chem. A, 121(12), 2503-2514 (2017).

J.F. Liu, L.W. Qi, John Z.H. Zhang, X. He, “Fragment Quantum Mechanical Method for Large-Sized Ion-Water Clusters”, J. Chem. Theory. Comput., 13(5), 2021-2034 (2017).

L.L. Duan, T. Zhu, Y.C. Li, Q.G. Zhang, John Z.H. Zhang, “Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations”, Sci. Rep., 7, 42223 (2017).

L.L. Duan, T. Zhu, C.G. Ji, Q.G. Zhang, John Z.H. Zhang, “Direct folding simulation of helical proteins using an effective polarizable bond force field”, Phys. Chem. Chem. Phys., 19(23), 15273-15284 (2017).