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D.W. Zhang and J.Z.H. Zhang, “Full quantum mechanical study of binding of HIV-1 protease drugs”, Int. J. Quant. Chem. 103, 246-257 (2005).
Y. Mei, D.W. Zhang, and J.Z.H. Zhang, “A new method for direct linear scaling calculation of electron density of protein”, J. Phys. Chem. A 109, 2 (2005) (Letter)
Xiao He and John Z.H. Zhang, “A new method for direct calculation of total energy of protein”, J. Chem. Phys. 122, 031103 (2005) (communication).
Y. Mei, X. He, Y. Xiang, D.W. Zhang, and J.Z.H. Zhang, “Quantum study of mutational effect in binding of Efavirenz to HIV-1 RT”, Proteins: Structure, Function and Bioinformatics 59, 489-495 (2005).
X. He, Y. Mei, Y. Xiang, D.W. Zhang, and J.Z.H. Zhang, “Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations”, Proteins: Structure, Function and Bioinformatics 61, 423-432 (2005).
Xi Hua Chen, Yingkai Zhang, and John Z.H. Zhang, “An efficient approach for energy calculation of biopolymers”, J. Chem. Phys. 122, 184105 (2005).
Q. Cui, M.L. Wang, J.Z.H. Zhang, “Effect of entrance channel topology on reaction dynamics: O+CH4 -> CH3O +Ｈ4”, Chem. Phys. Lett. 410,115-119 (2005).
L.P. Ju, K.L. Han, and J.Z.H. Zhang, “A theoretical study for H-2+CN ←→ HCN+H reaction and its kinetic isotope effects with variational transition state theory”, J. Theo. & Comput. Chem.: 5,769-777(2006).
Ye Mei, Emilia L. Wu, K.L. Han, and J.Z.H. Zhang, “Treating hydrogen bonding in ab initio calculation of biopolymers,” Int. J. Quant. Chem. 106, 1267-1276 (2006).
Y. Zhang, T.X. Xie, K.L. Han, J.Z.H. Zhang, “Nonadiabatic reactant-product decoupling calculation for the F(2P1/2)+H2 reaction”, J. Chem. Phys. 124, 134301 (2006).
X. He and J.Z.H. Zhang, “The generalized molecular fractionation with conjugate caps/molecular mechanics method for direct calculation of protein energy”, J. Chem. Phys. 124, 184703 (2006).
T.S. Chu, X. Zhang, L.P. Ju, L. Yao, K.L. Han, M.L. Wang, J.Z.H. Zhang, “First principles quantum dynamics study reveals subtle resonance in polyatomic reaction: The case of F+CH4→HF+CH3”, Chem. Phys. Lett. 424, 243-246 (2006).
S.A. Vail, D.I. Schuster, D.M. Guldi, M. Isosomppi, N. Tkachenko, H. Lemmetyinen, A. Palkar, L. Echegoyen, X.H. Chen, J.Z.H. Zhang, “Energy and electron transfer in beta-alkynyl-linked porphyrin-[60]fullerene dyads”, J. Phys. Chem. B 110, 14155-14166 (2006).
X.H. Chen and J.Z.H. Zhang, “Molecular fractionation with conjugated caps density matrix with pairwise interaction correction for protein energy calculation”, J. Chem. Phys. 125, 044903 (2006).
J. C. Varandas, P. J. S. B. Caridade, J. Z. H. Zhang, Q. Cui, and K. L. Han, “Dynamics of X+CH4 (X=H, O, Cl) reactions: How reliable is transition state theory for fine-tuning potential energy surfaces?”, J. Chem. Phys. 125, 064312 (2006).
Y. Mei, C.G. Ji, and J.Z.H. Zhang, “A new quantum method for electrostatic solvation energy of protein,” J. Chem. Phys. 125, 094906 (2006),
R.F. Lu, T.S. Chu, Y. Zhang, and K.L. Han, A.J.C. Varandas, and J.Z.H. Zhang, “Nonadiabatic effects in the H+D2 reaction,” J. Chem. Phys. 125, 133108 (2006).
Y.S. Wang, S. Sabu, S.C. Wei, C.M.J. Kao, X.L. Kong, S.C. Liau, C.C. Han, H.C. Chang, S.Y. Tu, A.H. Kung, J.Z.H. Zhang, “Dissociation of heme from gaseous myoglobin ions studied by infrared multiphoton dissociation spectroscopy and Fourier-transform ion cyclotron resonance mass spectrometry”, J. Chem. Phys. 125, 133310 (2006).
S. Lee-Huang, P.L. Huang, D. Zhang, J.W. Lee, J. Bao, Y. Sun, Y-Tae Chang, J. Zhang and P. L. Huang, “Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: Part I. Fusion inhibition”, Biochem. Biophys. Res. Commun. 354, 872-878 (2007).
S. Lee-Huang, P.L. Huang, D. Zhang, J.W. Lee, J. Bao, Y. Sun, Y-Tae Chang, J.Z.H. Zhang and P. L. Huang, “Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: Part II. Integrase inhibition”, Biochem. Biophys. Res. Commun. 354, 879-884 (2007).
Emilia L. Wu, Ye Mei, Ke L. Han, and John Z.H. Zhang, “Quantum computational study for binding of Oscillarin and two Macrocyclic inhibitors to human alpha thrombin using the MFCC method”, Biophys. J. 92, 4244 (2007).
Xu Q. Zhang, Q. Cui, Ke L. Han, J.Z.H. Zhang, “Quantum dynamics study of H + NH3 → H2 + NH2 reaction”, J. Chem. Phys. 126, 234304 (2007).
L.L. Duan, Y. Tong, Y. Mei, Q.G. Zhang, J. Z.H. Zhang, “Quantum study of HIV-1 protease-bridge water interaction”, J. Chem. Phys. 127, 145101 (2007).
J. Bao, D. W. Zhang, J. Z.H. Zhang, P. L. Huang, P.L. Huang, S. Lee-Huang, “Computational study of bindings of olive leaf extract (OLE) to HIV-1 fusion protein gp41”, FEBS Letters 581, 2737-2742 (2007).
Xi-Hua Chen and John Z. Zhang, “A non-derivative MFCC optimization study of cyclohexapeptide monohydrate”, Chinese J. Chem. Phys. 20, 431 (2007).
Yun Ding, Ye Mei, John Z.H.Zhang, and Fu-ming Tao, “Efficient bond function basis set for pi-pi interaction energies”, J. Comput. Chem. 29, 275 (2008).
C.G. Ji, Y. Mei and J.Z.H. Zhang, “Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin”, Biophysical Journal95, 1080 (2008).
E.L. Wu, K.L. Han and J.Z.H. Zhang, “Molecular Dynamics Study for the selectivity of Neutral/ Weakly Basic P1 groups inhibitors with Thrombin and Trypsin”, Chemistry-A European Journal14, 8704-8714 (2008)..
Y. Ding, Y. Mei, J.Z.H. Zhang, “Quantum mechanical studies of residue-specific hydrophobicinteractions in p53-MDM2 binding, J. Phys. Chem. B112, 11396-401 (2008).
D.W. Zhang, P.L. Huang, S. Lee-Huang, “Design of hybrid inhibitors to HIV-1 protease”, J. Theo. & Comput. Chem. 7, 485 (2008).
C.G. Ji and J.Z.H. Zhang, “Protein Polarization Is Critical to Stabilizing AF-2 and Helix-2’ Domains in Ligand Binding to PPARgamma”, J. Am. Chem. Soc. 130, 17129–17133 (2008).
M. Han and J.Z.H. Zhang, “Molecular Dynamic Simulation of Kv1.2 Voltage-gatedPotassium Channel in Open and Closed State Conformations”, J. Phys. Chem. B112, 16966–16974 (2008).
L.L. Duan, Y. Mei, Q.G. Zhang, and J.Z.H. Zhang, “Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization”, J. Chem. Phys. 130, 115102 (2009).
Li-Ping Ju, K.L. Han, J. Z.H. Zhang, “Global Dynamics and Transition State Theories: Comparative Study of Reaction Rate Constants for Gas-Phase Chemical Reactions”, J. Comput. Chem. 30, 305-316 (2009).
Y. Tong, C.G. Ji, Y. Mei, J.Z.H. Zhang, “Simulation of NMR Data Reveals that Protein’s local structures Are Stabilized by Electronic Polarization”, J. Am. Chem. Soc. 131, 8636–8641 (2009).
J. Bao, X.Y. Dong, J.Z.H. Zhang, P.S. Arora, “Dynamical Binding of Hydrogen-Bond Surrogate Derived Bak Helices to Antiapoptotic Protein Bcl-x(L)”, J. Phys. Chem. B113, 3565-3571(2009).
E.L. Wu, K.L. Han, J.Z.H. Zhang, “Computational Study for Binding of Oscillarin To Human Alpha-Thrombin”, J. Theo. & Comput. Chem.8, 551-560(2009).
C.G. Ji and J.Z.H. Zhang, “NMR Scalar Coupling Constant Reveals That Intraprotein Hydrogen Bonds Are Dynamically Stabilized by Electronic Polarization”, J. Phys. Chem. B, 113,13898-13900(2009).
C.G. Ji and J.Z.H. Zhang, “Electronic Polarization Is Important in Stabilizing the Native Structures of Proteins,” J. Phys. Chem. B, 113,16059–16064(2009).
Y. Mei and J.Z.H. Zhang, “Numerical Stabilities in Fitting Atomic Charges to Electric Field and Electrostatic Potential”, J. Theo. Comput. Chem. 8, 925-942 (2009).
Y.L. Li, L. Han, Y. Mei, and J.Z.J. Zhang, “Time-dependent density functional theory study of absorption spectra of metallocenes”, Chem. Phys. Letts. 482,217-222(2009).
Y. Tong, Y. Mei, J.Z.H. Zhang, L.L. Duan, Q.G. Zhang, “Quantum calculation of protein solvation and protein–ligand binding free energy for hiv-1 protease/water complex”, J. Theo. Comput. Chem. 8, 1265-1279 (2009).
H.G. Li, P.L. Huang, D.W. Zhang, Y.T. Sun, H.C. Chen, J. Zhang, P.L. Huang, X.P. Kong, S. Lee-Huang, “A new activity of anti-HIV and anti-tumor protein GAP31: DNA adenosine glycosidase - Structural and modeling insight into its functions”, Biochem. Biophys. Res. Commun., 391, 340-345(2010).
M. Han and J.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. Info. Mod.50,136-145(2010).
Y. Tong, Y. Mei, Y.L. Li, C.G. Ji, J.Z.H. Zhang, “Electrostatic polarization makes substantial contribution to free energy of avidin-biotin binding, J. Am. Chem. Soc. 132, 5137-5142 (2010).
Yunpeng Lu, Y. Mei, J.Z.H. Zhang, Dawei Zhang, “Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase”, J. Chem. Phys. (Communications), 132, 131101 (2010).
L.L. Duan, Y. Mei, Y.L. Li, Q.G. Zhang, D.W. Zhang, J.Z.H. Zhang, “Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models”, Science China-Chemistry 53, 196-201 (2010).
Li L. Duan,Ye Mei,Dawei Zhang, Qing G. Zhang, and John Z. H. Zhang, “Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds”, J. Am. Chem. Soc. 132, 11159–11164 (2010).
P. Wang and J.Z.H. Zhang, “Selective Binding of Anti-influenza Drugs and Their Analogues to 'Open' and 'Closed' Conformations of H5N1 Neuraminidase”, J. Phys. Chem. B114, 12958-12964(2010).
D.W. Zhang, L.Z. Yu, P.L. Huang, P.L. Huang, S. Lee-Huang, J.Z.H. Zhang, “COMPUTATIONAL DESIGN OF NORBORNANE-BASED HIV-1 PROTEASE INHIBITORS”, J. Theo. Comput. Chem. 9, 471-485 (2010).
Y. Xiang, L.L. Duan, J.Z.H. Zhang, “Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy”, Phys. Chem. Chem. Phys. 12, 15681-15688(2010).
X. Y. Wang and J.Z.H. Zhang, “Effect of polarization on the stability of a helix dimer”, Chem. Phys. Lett. 501, 508-512 (2011).
Y. Xiang, L.L. Duan, J.Z.H. Zhang, “Protein’s electronic polarization contributes significantly to its catalytic function”, J. Chem. Phys. 134, 205101 (2011).
Y. L. Li, Yong, Y. Mei, D.W. Zhang, D.Q. J.Z.H. Zhang, “Structure and Dynamics of a Dizinc Metalloprotein: Effect of Charge Transfer and Polarization”, J. Phys. Chem. B115, 10154-10162 (2011).
K.Z. Song, J. Bao, Y.M. Sun, J.Z.H. Zhang, “Computational Characterization of Binding of Small Molecule Inhibitors to HIV-1 gp41”, Chin. J. Chem. 29, 1307-1311 (2011).
C.G. Ji and J.Z.H. Zhang, “Quantifying the Stabilizing Energy of the Intra-protein Hydrogen Bond Due to Local Mutation”, J. Phys. Chem. B115, 12230–12233 (2011).
C.G. Ji and J.Z.H. Zhang, “Understanding the Molecular Mechanism of Enzyme Dynamics of Ribonuclease A through Protonation/Deprotonation of HIS48”, J. Am. Chem. Soc. 133, 17727-17737 (2011).
Y. Mei, D.W. Zhang, L.L. Duan, etc., “Folding of EK peptide and its dependence on salt concentration and pH: A computational study”, Science China-Chemistry, 54, 1974-1981 (2011).
Y. Gao, Lu, X. L., Duan, L. L., Zhang, J. Z. H, Mei, Y., “Polarization of Intraprotein Hydrogen Bond Is Critical to Thermal Stability of Short Helix”, J. Phys. Chem. B, 2011, 116, 1 549-554 (2012).
Tong Zhu, Xiao He and John Z.H. Zhang, “Fragment density functional theory calculation of NMR chemical shift for proteins with implicit salvation”, Phys. Chem. Chem. Phys.14, 7837 (2012).
L.L. Duan, Y. Gao, Y. Mei, Q.G. Zhang, B. Tang, J.Z.H. Zhang, “Folding of a Helix is Critically Stabilized by Polarization of Backbone Hydrogen Bonds: Study in Explicit Water”,Journal of Physical Chemistry B, 116, 3430 (2012).
Ya Gao, Guo, M.，Ye Mei, and John Z.H. Zhang, “Protein-Water Hydrogen Bonds are Stabilized by Electrostatic Polarization”, Molecular Physics, 110, 595 (2012).
C.G. Ji and J.Z.H. Zhang, “Effect of inter-protein polarization on protein-protein binding energy”, J. Comput. Chem., 33, 16,1416–1420（2012）.
Ye Mei, Yong L. Li, Juan Zeng, and John Z.H. Zhang, “Electrostatic polarization is critical for the strong binding in streptavidin-biotin system”, J. Comput. Chem., 33, 1374 (2012).
Ye Mei, Xiao He, Chang G. Ji, and John Z.H. Zhang, “A Fragmentation Approach to Quantum Calculation of Large Molecular Systems”, Progress in Chemistry, 24, 1058 (2012).
Weixin Xu, Li Yang; Zhang, John Z. H.，Calculation of Collective Variable-based PMF by Combining WHAM with Umbrella Sampling，Chinese Physics Letters, Vol. 29, 068702, (2012).
Weixin Xu, Haibin Su, John Z. H. Zhang, Yuguang Mu, Molecular Dynamics Simulation Study on the Molecular Structures of the Amylin Fibril Models, J. Phys. Chem. B, 116，13991-13999, 2012
Chang G. Ji, Xudong Xiao,and John Z. H. Zhang,Studying the Effect of Site-Specific Hydrophobicity and Polarization on Hydrogen Bond Energy of Protein Using a Polarizable Method,J. Chem. Theory Comput., 8 (6), pp 2157–2164(2012).
Mei, Y.,Wei, C. Y.,Yip, Y. M.,Ho, C. Y., Zhang, J. Z. H., Zhang, D. W., “Folding and thermodynamic studies of Trp-cage based on polarized force field”, Theoretical Chemistry Accounts, 131, 1168 (2012).
Jiang, Biao,Han, Lei, Li, Yong-Le, Xiao-Long Zhao,Yang Lei,Dai-Qian Xie,and John Z. H. Zhang, “Combined Theoretical and Experimental Study on High Diastereoselective Chirality Transfer Based on [2.2]Paracyclophane Derivative Chiral Reagent,Journal of Organic Chemistry,77 , 4 , 1701-1709 (2012).
Jun Xu,John Z. H. Zhang,and Yun Xiang, “Ab Initio QM/MM Free Energy Simulations of Peptide Bond Formation in the Ribosome Support an Eight-Membered Ring Reaction Mechanism”，J. Am. Chem. Soc., 134, 16424?16429 (2012)
Xing Y. Wang, Chang G. Ji, and John Z. H. Zhang，“Exploring the Molecular Mechanism of Stabilization of the Adhesion Domains of Human CD2 by N-Glycosylation”，J. Phys. Chem. B, 116 (38), pp 11570–11577（2012).
Yang Li , Changge Ji , Weixin Xu , and John Z.H. Zhang,“Dynamical Stability and Assembly Cooperativity of β-Sheet Amyloid Oligomers – Effect of Polarization”, J. Phys. Chem. B, 116, 13368–13373（2012).
X. Xiao, T. Zhu, C.G Ji, J.Z.H. Zhang, “Development of an Effective Polarizable Bond Method for Biomolecular Simulation”, J. Phys. Chem. B 117 (48), 14885-14893 (2013).
J.N. Song, C.G. Ji, and J.Z.H. Zhang, “Unveiling the gating mechanism of ECF Transporter RibU”, Scientific Reports, 3, 3566 (2013).
Ren, S., Zeng, J., Mei, Y., Zhang, J. Z. H., Yan, S. F., Fei, J.,Chen, L., “Discovery and characterization of novel, potent, and selective cytochrome P450 2J2 inhibitors”, Drug Metabolism and Disposition, 41, 60-71 (2013)
S.Y. Lin, P.Y. Zhang, J.Z.H. Zhang, “Hybrid many-body-expansion/Shepard-interpolation method for constructing ab initio potential energy surfaces for quantum dynamics calculations”, Chem. Phys. Letts., 556, 393-397 (2013).
Jianing Song, C.G. Ji, J.Z.H. Zhang, “The critical effect of polarization on the dynamical structure of guanine quadruplex DNA”, Phys. Chem. Chem. Phys., 15, 3846-3854 (2013).
Z. Juan; Duan, Li Li; Zhang, John Z. H., Y. Mei, A numerically stable restrained electrostatic potential charge fitting method, J. Comput. Chem. 34(10), 847-853 (2013). .
Zhang, SQ , Mu, YG ,Zhang, JZH ; ,Xu, WX , “Effect of Self-Assembly of Fullerene Nano-Particles on Lipid Membrane, PLOS ONE , 8,10 (2013).
Lu, XL ; Zeng, J ; Gao, Y ; Zhang, JZH; Zhang, DW ; Mei, Y , “The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: a replica exchange molecular dynamics study”, J. Mol. Model., 19 ,4897-4908 (2013).
Zeng, J ;Jia, XY ;Zhang, JZH; Mei, Y, “The F130L Mutation in Streptavidin Reduces Its Binding Affinity to Biotin through Electronic Polarization Effect”, J. Comput. Chem., 34, 2677-2686 (2013).
Yang Li; Weixin Xu; Yuguang Mu; John Z. H. Zhang, Acidic pH retards the fibrillization of human islet amyloid polypeptide due to electrostatic repulsion of histidines. J. Chem. Phys. 139, 5 (2013).
Xu, Weixin; Zhang, Ce; Morozova-Roche, Ludmilla; Mu, Yuguang; Zhang, John Z. H., pH-Dependent Conformational Ensemble and Polymorphism of Amyloid-beta Core Fragment, J. Phys. Chem. B. 117, 8392-8399 (2013).
Li, Y. X.; Gao, Y.; Zhang, X. Q.; Wang, X. Y.; Mou, L. R.; Duan, L. L.; He, X.; Mei, Y.; Zhang, J.Z.H., A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation, J. Mol. Model., 29, 3647-3657 (2013).
J. Bao, J.F. Liu, X.He; J.Z.H. Zhang,” Computational Study of HIV-1 gp41 NHR trimer: Inhibition Mechanisms of N-Substituted Pyrrole Derivatives and Fragment-Based Virtual Screening”, J. Theor. Comput. Chem., 12(6), 13411 (2013).
Ya Gao; Xiaoliang Lu; Lili Duan; Dawei, Zhang; Ye, Mei; John, Z. H. Zhang, Direct folding simulation of a long helix in explicit water. Appl. Phys. Lett. 102,193706 (2013).
Liu, Jinfeng; He, Xiao; Zhang, John Z. H., 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).
Xu, J, Zhang, J.Z.H., Xiang, Y, “Molecular Dynamics Simulation and Computational Two-Dimensional Infrared Spectroscopic Study of Model Amyloid beta-Peptide Oligomers”, J. Phys. Chem. A, 117, 6373-6379 (2013).
Yao Xue Xia; Ji Chang Ge; Xie Dai Qian; Zhang, John Z. H. , Interaction specific binding hotspots in endonuclease colicin-immunity protein complex from MD simulations. Sci. China. Chem. 56, 1143-1151 (2013).
Wang, XW ; He, X ; Zhang, J.Z.H.,” Predicting Mutation-Induced Stark Shifts in the Active Site of a Protein with a Polarized Force Field”, J. Phys. Chem. A, 117, 6015-6023 (2013)
Duan, L. L.; Zhu, T.; Mei, Y.; Zhang, Q. G.; Tang, B.; Zhang, J. Z. H., An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins. J. Mol. Model., 19, 2605-2612 (2013).
Wang, XW ; Liu, JF ;Zhang, JZH; He, X,” Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method for Full Quantum Mechanical Calculation of Protein Energy”, J. Phys. Chem. A, 32, 7149-7161 (2013).
T. Zhu, J.Z.H. Zhang and X. Xiao, Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model. J. Chem. Theory Comput. 9, 2104 (2013),
Zhu, T ; Xiao, XD ; Ji, CG ; Zhang, J.Z.H., “A New Quantum Calibrated Force Field for Zinc-Protein Complex”, J. Chem. Theory Comput.,9, 1788-1798 (2013).
Jia, Xiangyu; Zhang, John Z. H.; Mei, Ye, Assessing the accuracy of the general AMBER force field for 2,2,2-trifluoroethanol as solvent, J. Mol. Model., 19, 2355-2361 (2013).
Yao, Xue X.; Ji, Chang G.; Xie, Dai Q.; Zhang, John Z. H.,Molecular dynamics study of DNA binding by INT-DBD under a polarized force field, J. Comput. Chem., 34, 1136-1142 (2013).
Xiangyu Jia, Xianwei Wang, Jinfeng Liu, John Z. H. Zhang, Ye Mei，and Xiao He, “An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins”, J. Chem. Phys., 139, 214104 (2013).
Li Yongxiu; Zhang J.Z.H; Mei Ye, Molecular Dynamics Simulation of Protein Crystal with Polarized Protein-Specific Force Field. J. Phys. Chem. B. 118, 12326(2014).
Duan LL; Gao Y; Ji CG; Mei Y; Zhang QG; Tang B; Zhang John Z.H., Energetics of protein backbone hydrogen bonds and their local electrostatic environment. Sci. China-Chemistry. 57, 1708-1715 (2014).
Min Li; Weixin Xu; John Z.H. Zhang; Fei Xia, Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase. J. Mol. Model. 20, 2530 (2014).
Wang Xianwei; Li Yongxiu; He Xiao; Chen SD; Zhang, John, JZH, Effect of strong electric field on the conformational integrity on insulin, J. Phys. Chem. A. 118(39). 8942-8952 (2014).
Liu,Jinfeng; He Xiao; Zhang, John Z. H., Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine, J. Mol. Model, 20(10), 2450 (2014).
Tong Zhu, John Z. H. Zhang and Xiao He, Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculation Phys. Chem. Chem. Phys. 16(34), 18163-18169 (2014).
Xiao He, Tong Zhu, Xianwei Wang, JInfeng Liu, and John Z. H. Zhang, Fragment quantum mechanical calculation of proteins and its applications Acc. Chem. Res.47(9) 2748-2757 (2014).
Jiali Gao, John Z. H. Zhang, Kendall N Houk, Beyond QM/MM: Fragment quantum mechanical methods Acc. Chem. Res. 47(9), 2711-2711 (2014).
Lirong Mou; Xiangyu Jia; Ya Gao; Yongxiu Li; Zhang J.Z.H; Ye Mei, Folding simulation of Trp-cage utilizing a new AMBER comatible force field with coupled main chain torsion J. Theor. Comput. Chem., 13. 1450026 (2014).
Kunzhong Song; Ju Bao; Yueming Sun; Zhang, J.Z.H., “Binding of N-substituted pyrrole derivatives to HIV-1 gp41”,J. Theor.Comput. Chem.,13(2):1450018 (2014).
Duan, L.L.; Ye Mei; Zhang, Q.G.; Bo Tang; Zhang, J.Z.H., “Protein's native structure is dynamically stabilized by electronic polarization”, J. Theor. Comput. Chem.,13, 1440005 (2014).
Zhang, Lujia; Gao, Bei; Yuan, Zuanning; He, Xiao; Yuan, Y Adam; Zhang, John Z H; Wei, Dongzhi, “Structure, mechanism, and enantioselectivity shifting of lipase LipK107 with a simple way”, Biochimica et biophysica acta,1844(7):1183-92 (2014).
Duan LL, Zhu T, Zhang QG, Tang B, Zhang JZH., “Electronic polarization stabilizes tertiary structure prediction of HP-36”, J. Mol. Model., 20(4):2195 (2014).
Lin B. B.; Gao Y.; Li Y. X; Zhang J. Z. H.; Mei Y., “Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of Myoglobin”, J. Mol. Model., 20, 2189 (2014).
Jia, Xiangyu; Zeng, Juan; Zhang, John Z. H.; et al. “Accessing the Applicability of Polarized Protein-Specific Charge in Linear Interaction Energy Analysis, J. Comput. Chem. 35(9): 737-749 (2014).
Song, Jianing; Ji, Changge; Zhang, John Z. H., “Insights on Na+ binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM”,Proteins: Structure, Function, and Bioinformatics. 82(2): 240-249 (2014).
Ji, Chang G.; Mei, Ye; Zhang, John Z. H., “Protein structure and dynamics-polarization in MD simulation”, Abstr. Am. Chem. Soc. 248 (2014).
Min Li; John Z.H. Zhang; Fei Xia, Heterogeneous elastic network model improves description of slow motions of proteins in solution, Chem. Phys. Lett. 618(2), 102 (2015).
Zhu, Tong; Zhang, John Z. H.; He, Xiao, “Quantum Calculation of Protein NMR Chemical Shifts Based on the Automated Fragmentation Method”,Adv. Exp. Med. Biol. 827: 49-70 (2015).
Zhu, Tong; He, Xiao; Zhang, John Z. H.,”Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation” Phys. Chem. Chem. Phys.,17,18:12367-12367 (2015).
Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H., “Functional Loop Dynamics of the Streptavidin-Biotin Complex”,Sci. Rep., 5, 7906 (2015).
Li, Yongxiu; Zhang, John Z. H.; Mei, Ye, “Molecular Dynamics Simulation of Protein Crystal with Polarized Protein-Specific Charge”, Biophys. J., 108, 2: 160A-160A (2015).
Gao, Ya; Li, Yongxiu; Zhang, JZH; Mei, Ye, “A Coupled Two-Dimensional Main Chain Torsional Potential for Protein Dynamics”,Biophys. J., 108, 2:159A-160A (2015).
Gao, Ya; Li, Yongxiu; Mou, Lirong; Hu, Wenxin; Zheng, J; Zhang, JZH; Mei, Y, “Coupled Two-Dimensional Main-Chain Torsional Potential for Protein Dynamics II: Performance and Validation”,J. Phys. Chem. B, 119,11: 4188-4193(2015).
Gao, Ya; Li, Yongxiu; Mou, Lirong; Lin, BB; Zhang, JZH; Mei, Y, “Correct folding of an alpha-helix and a beta-hairpin using a polarized 2D torsional potential”, Sci. Rep.,5 ,10359 (2015).
Wang, Xingyu; Ji, Chang G.; Zhang, John Z. H., “Glycosylation Modulates Human CD2-CD58 Adhesion via Conformational Adjustment”,J. Phys. Chem. B, 119, 22: 6493-6501(2015).
Yang, Junru; Song, Jianing; Zhang, JZH; Ji, CG, “Effect of mismatch on binding of ADAR2/GluR-2 pre-mRNA complex”,J. Mol. Model., 21, 9(2015).
Chen, JZ; Wang, XY; Zhu, T; Zhang, QG; Zhang, JZH, “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).
Wang, Xianwei; Zhang, John Z. H.; He, Xiao, “Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase”, J. Chem. Phys., 143, 18, 184111(2015).
Xiangyu Jia, Ye Mei, John Z.H. Zhang, Yan Mo, “Hybrid QM/MM study of FMO complex with polarized proteinspecific charge”, Sci. Rep., 5,17096(2015).
Jinfeng Liu, Tong Zhu, Xianwei Wang, Xiao He and John Z. H. Zhang, “Quantum Fragment Based ab Initio Molecular Dynamics for Proteins”, J. Chem. Theory Comput. 11, 5897?5905 (2015).
Jinfeng Liu, Xianwei Wang, John Z. H. Zhang and Xiao He, “Calculation of protein–ligand binding affinities based on a fragment quantum mechanical method”, RSC Adv., 5, 107020(2015).
J.F. Liu, J.Z.H. Zhang, X. He, “Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins”, Phys. Chem. Chem. Phys., 18, 1864-1875 (2016).
X.Y. Jia, M.T. Wang, Y.H. Shao, G. K?nig, B.R. Brooks, J.Z.H. Zhang, Y. Mei, “Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics”, J. Chem. Theory Comput., 12, 499–511 (2016).
M. Li, J.Z.H. Zhang, F. Xia, “A new algorithm for construction of coarse-grained sites of large biomolecules”, J. Comput. Chem., 37, 795–804 (2016).
X. Liu, J.F. Liu, T. Zhu, L.J. Zhang, X. He, and J.Z.H. Zhang, “PBSA_E: A PBSA-Based Free Energy Estimator for Protein–Ligand Binding Affinity”, J. Chem. Inf. Model., 56, 854-861 (2016).
L.L. Duan, X. Liu, J.Z.H. Zhang, “Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free Energy”, J. Am. Chem. Soc., 138, 5722–5728 (2016).
Y. Liu, Z.Z. Yu, J.Z.H. Zhang, L. Liu, F. Xia, J.L. Zhang, “Origins of unique gold-catalysed chemo-and site-selective C–H functionalization of phenols with diazo compounds”, Chem. Sci., 7, 1988-1995 (2016).
Y. Liu, Z.Z. Yu, Z.J. Luo, J.Z.H. Zhang, L. Liu, F. Xia, “Mechanistic Investigation of Aromatic C (sp2)–H and Alkyl C (sp3)–H Bond Insertion by Gold Carbenes”, J. Phys. Chem. A, 120(11), 1925-1932 (2016).
M. Li, J.Z.H. Zhang, F. Xia, “Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization”, J. Chem. Theory Comput., 12(4), 2091-2100 (2016).
X.W. Wang, X. He, J.Z.H. Zhang, “Accurate Calculation of Electric Fields Inside Enzymes”, Methods in Enzymology, 578, 45-72 (2016).
Y. Wang, J.F. Liu, T. Zhu, L.J. Zhang, X. He, J.Z.H. Zhang, “Predicted PAR1 inhibitors from multiple computational methods”, Chem. Phys. Lett., 659, 295-303 (2016).
M. Li, F.J. Liu, J.Z.H. Zhang, “TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein”, J. Chem. Theory Comput. 12, 6147-6156 (2016).
F.J. Liu, J.Z.H. Zhang, Y. Mei, “The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations”, Sci. Rep., 6, 27190 (2016).
Y.X. Li, S.Q. Zhang, J.Z.H. Zhang, X. He, “Assessing the performance of popular QM methods for calculation of conformational energies of trialanine”, Chem. Phys. Lett., 652, 136-141 (2016).
Z.Q. Yao, L.J. Zhang, B. Gao, D.B. Cui, F.Q. Wang, X. He, J.Z.H. Zhang, D.Z. 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, 1979-1994 (2016).
J. Zeng, Y.X. Li, J.Z.H. Zhang, Y. Mei, “Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88”, J. Mol. Model., 22, 177 (2016).
B. Peng, X.Y. Ding, C. Sun, W. Liu, J.Z.H. Zhang, X. Zhao, “The effect of POPC acyl chains packing by aromatic amino acid methyl esters investigated by ATR-FTIR combined with QM calculations”, RSC Adv., 6, 45569-45577 (2016).
Y. Liu, Z.J. Luo, J.Z.H. Zhang, F. Xia, “DFT Calculations on the Mechanism of Transition-Metal-Catalyzed Reaction of Diazo Compounds with Phenols: O-H Insertion versus C-H Insertion”, J. Phys. Chem. A, 120, 6485-6492 (2016).
J.F. Liu, Y.Q. Wang, Z.H. Zhang, X. He, “Quantum mechanical mechanism of binding of 4‐anilinoquinazoline inhibitors to the epidermal growth factor receptor based on MFCC computation”, China Sciencepaper, 11(18), 2050-2056 (2016).
X.S. Jin, T. Zhu, J.Z.H. Zhang, X. He, “A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach”, RSC Adv., 6, 108590-108602 (2016).
Z.X. Sun, X.H. Wang and John Z. H. Zhang, “BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation”, Phys.Chem.Chem.Phys.,19, 15005 (2017).
Y. Wang, J.F. Liu, L.J. Zhang, X. He, John Z.H. Zhang, “Computational search for aflatoxin binding proteins”, Chem. Phys. Lett., 685, 1-8 (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).
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).
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).
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).
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).
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, 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).
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).
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).
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).
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, 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).
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).
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).
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).
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).
Wang, XW; Zhang, JZH; He, X, “Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin”, Chin. J. Chem. Phys. 30, 705-716 (2017).
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 (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, doi: 10.3389/fchem.2018.00380 (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).
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).
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, DOI: 10.3389/fchem.2018.00150 (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, DOI: 10.1038/s41598-018-24760-x (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.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).
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, 19-20, 2613-2621 (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, 19-20, 2633-2641 (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).
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).
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).
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).
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).
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).
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).
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.N. Song, L.Q. Song, J.Z.H. Zhang, “An efficient method for computing excess free energy of liquid”, Science China-Chemistry, 61, 12, 1638 (2018).
J.Z. Chen, X.Y. Wang, J.Z.H. Zhang, T. Zhu, “Effect of Substituents in Different Positions of Aminothiazole Hinge-Binding Scaffolds on Inhibitor-CDK2 Association Probed by Interaction Entropy Method”, ACS Omega, 3, 18052-18064 (2018).
Y.C. Li, Y.L. Cong, G.D. Feng, S.S. Zhong, J.Z.H. Zhang, H.Y. Sun, L.L. Duan, “The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction”, Structural Dynamics-US, 5, 064101 (2018).
Chih-Hao Chin, T. Zhu, J.Z.H. Zhang, “Formation mechanism and spectroscopy of C6H radicals in extreme environments: a theoretical study”,Phys. Chem. Chem. Phys., 21, 23044-23055 (2019).
S.Z. Tian, J.Z. Zeng, X. Liu, J.Z. Chen, J.Z.H. Zhang, T. Zhu, “Understanding the selectivity of inhibitors toward PI4KIIIa and PI4KIIIb based molecular modeling”, Phys. Chem. Chem. Phys., 21, 22103-22112 (2019).
Z.R. Xiao, Y.L. Cong, K.F. Huang, S.S. Zhong, J.Z.H. Zhang. L.L.Duan, “Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy”, Phys. Chem. Chem. Phys., 21, 20951-20964 (2019).
J. Chen, H. Gao, T. Ding, L.Z. Ji, J.Z.H. Zhang, G.H. Gao, F. Xia, “Mechanistic Studies of CO2 Cycloaddition Reaction Catalyzed by Amine-Functionalized Ionic Liquids”,Front. Chem., 7, 615 (2019).
G.F. Duan, C.G. Ji, J.Z.H. Zhang, “A force consistent method for electrostatic energy calculation in fluctuating charge model”, J. Chem. Phys., 151, 094105 (2019).
L.P. He, J.X. Bao, Y.P. Yang, S.Z. Dong, L.J. Zhang, Y.F. Qi, J.Z.H. Zhang, “Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning”, J. Chem. Inf. Model., 59, 3871?3878 (2019).
E.C. Wang, H.Y. Sun, J.M. Wang, Z. Wang, H. Liu, J.Z.H. Zhang, T.J. Hou, “End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design”, Chem. Rev., 119, 9478?9508 (2019).
L.L. Duan, X.N. Guo, Y.L. Cong, G.Q. Feng, Y.C. Li, J.Z.H. Zhang, “Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water”, Front. Chem., 7, 540 (2019).
M.Y. Xu, T. Zhu, J.Z.H. Zhang, “Molecular Dynamics Simulation of Zinc Ion in Water with an ab Initio Based Neural Network Potential”, J. Phys. Chem. A, 123, 6587?6595 (2019).
J.Z. Chen, X.Y. Wang, L.X. Pang, J.Z.H. Zhang, T. Zhu, “Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations”, Nucleic Acids Research, 47, 13, 6618-6631 (2019).
Z.X. Sun, X.H. Wang, J.Z.H. Zhang, Q.L. He, “Sulfur-substitution-induced base flipping in the DNA duplex”, Phys. Chem. Chem. Phys., 21, 14923-14940 (2019).
Z.X. Sun, , X.H. Wang, J.Z.H. Zhang, “Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation”, Chem. Phys. Lett. 723, 1–10 (2019).
X.H. Wang, X.Z. Tu, B.M. Deng, J.Z.H. Zhang, Z.X. Sun, “BAR-Based Optimum Adaptive Steered MD for Configurational Sampling”, J. Comput. Chem., 40, 1270–1289 (2019).
D.D. Huang, Y.F. Qi, J.N. Song, J.Z.H. Zhang, “Calculation of Hot Spots for Protein–Protein Interaction in p53/PMI-MDM2/MDMX Complexes”, J. Comput. Chem., 40, 1045–1056 (2019).
M.Y. Xu, X. He, T. Zhu, J.Z.H. Zhang, “A Fragment Quantum Mechanical Method for Metalloproteins”, J. Chem. Theory Comput., 15, 1430?1439 (2019).
D.D. Huang, W. Wen, X. Liu, Y. Li, J.Z.H. Zhang*, “Computational analysis of hot spots and binding mechanism in the PD-1/PD-L1 interaction”, RSC Adv., 9, 14944–14956 (2019).
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., 59, 272?281 (2019).
Cao, Huali; Wang, Jingxue; He, Liping; Qi, Yifei*; Zhang, John Z.H.*, DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks, J. Chem. Inf. Model, 2019. 59(4), 1508~1514.
Liu, Xiao; Zhao, Yang*; Zhang, John Z.H.*, Molecular mechanism of ligand bindings to Zika virus at SAM site, Chem. Phys. Letts., 2019, 735,136771.
Yang, Yun-peng; He, Li-ping; Bao, Jing-xiao; Qi, Yi-fei*; Zhang, John Z. H.*, Computational Analysis for Residue-Specific CDK2-Inhibitor Bindings, Chinese J. Chem. Phys. 2019, 32(1)：134~142.
Wu, Zhenliang; Zhang, Yuwei; Zhang, John Zenghui; Xia, Kelin*; Xia, Fei*, Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes, J. Comput. Chem., 2019 , 41(1)：14~20.
Jianzhong chen* , Baohua Yin, Laixue Pang, Wei Wang, John Z. H. Zhang, Tong Zhu*, Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies, Journal of Biomolecular Structure and Dynamics, 2019, 38:7, 2141-2155.
Jianzhong Chen*, Laixue Pang, Wei Wang, Lifei Wang, John Z. H. Zhang, Tong Zhu*, Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations, Journal of Biomolecular Structure and Dynamics, 2019, 38:4, 985-996.
Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu*, John Z. H. Zhang*, Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation, Nature Communications, 2020, 11, 5713.
Bo Wang, Cuiyu Li, Jia Xiangyu, Tong Zhu,* John Z. H. Zhang*，An Approach to Computing Solvent Reorganization Energy, J. Chem. Theory Comput., 2020, 16, 6513?6519.
Cuiyu Li, Chih-Hao Chin* , Tong Zhu, John Zeng Hui Zhang*, An ab initio/RRKM study of the reaction mechanism and product branching ratios of CH3OHt and CH3OHtt dissociation, Journal of Molecular Structure, 2020, 1217, 128410.
Cuiyu Li, Bo Wang, Xiangyu Jia, John Z.H. Zhang*, Efficient calculation of excess free energy of pure and mixed alcohol solutions, Chemical Physics Letters, 2020, 749, 137397.
Kaifang Huang, Song Luo, Yalong Cong, Susu Zhong, John Z. H. Zhang, Lili Duan*, An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein–ligand binding affinity, Nanoscale, 2020, 12, 10737–10750.
Xiaolin Li, Yalong Cong, Mingzhe Ma, Zhi-Neng You, Bei Gao, John Z. H. Zhang*, Lujia Zhang*, An Energy Optimization Strategy Based on the Perfect Conformation of Prolyl Endopeptidase for Improving Catalytic Efficiency, J. Agric. Food Chem., 2020, 68, 5129?5137.
Bo Wang, Yifei Qi, Ya Gao*, John Z. H. Zhang*, A method for efficient calculation of thermal stability of proteins upon point mutations, Phys. Chem. Chem. Phys., 2020, 22, 8461.
Guanfu Duan, Changge Ji*, John Z. H. Zhang*, Developing an effective polarizable bond method for small molecules with application to optimized molecular docking, RSC Adv., 2020, 10, 15530.
Ran Wang , Yalong Cong, Mengxin Li, Jinxiao Bao, Yifei Qi*, John Z. H. Zhang*, Molecular Mechanism of Selective Binding of NMS-P118 to PARP-1 and PARP-2: A Computational Perspective, Front. Mol. Biosci., 2020, 7, 50.
Yalong Cong, Kaifang Huang, Yuchen Li, Susu Zhong, John Z. H. Zhang*, Lili Duan*, Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin–biotin binding, Nanoscale, 2020, 12, 7134–7145.
Chih-Hao Chin*, Tong Zhu*, John Zeng-Hui Zhang, Reaction mechanism and product branching ratios of OH+C2H3F reaction: A theoretical study, Chinese Journal of Chemical Physics, 2020, 33, 203-209.
Yifei Qi*, John Z. H. Zhang, DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet, J. Chem. Inf. Model. 2020, 60, 1245?1252.
Zhendong Li, Jingxiao Bao, Yifei Qi*, John Z. H. Zhang*, Computational approaches to studying methylated H4K20 recognition by DNA repair factor 53BP1, Phys. Chem. Chem. Phys., 2020, 22, 6136--6144.
Yalong Cong, Lili Duan*, Kaifang Huanga, Jinxiao Baob, John Z. H. Zhang*, Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor, Journal of Biomolecular Structure and Dynamics, 2020, 39, 1588-1599
Shuaizhen Tian, Changge Ji*, John Z. H. Zhang*, Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarization, Journal of Biomolecular Structure and Dynamics, 2020, 39, 743-752.
Zhaoxi Sun*, Xiaohui Wang, John Z. H. Zhang*, Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR–ligand binding, Phys. Chem. Chem. Phys., 2020, 22, 1511-1524.
Dading Huang, Shuaizhen Tian , Yifei Qi* ,John Z. H. Zhang*,Binding Modes of Small‐Molecule Inhibitors to the EED Pocket of PRC2, Chem. Phys. Chem., 2020, 21, 263–271.
Jinzhe Zeng, Liqun Cao, Chih-Hao Chin*, Haisheng Ren*, John Z. H. Zhang, Tong Zhu, ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations, Phys. Chem. Chem. Phys., 2020, 22, 683-691.
Min Li*, WenCai Lu, John Z.H. Zhang, A three-point coarse-grained model of five-water cluster with permanent dipoles and quadrupoles, Phys. Chem. Chem. Phys.,2020, 22, 26289.
Jingxiao Bao, Xiao He*, John Z.H. Zhang*, Development of a New Scoring Function for Virtual Screening: APBScore, J. Chem. Inf. Model., 2020, 60, 6355?6365.
Yanfang Han, Liping He, Yifei Qi, Yue Zhao, Yue Pan, Bohuan Fang, Sha Li, John Z. H. Zhang*, Lujia Zhang*, Identification of three new compounds that directly target human serine hydroxymethyltransferase 2, Chem Biol Drug Des. 2021, 97, 221-230.
Lili Duan*, Shuheng Dong, Kaifang Huang, Yalong Cong, Song Luo and John Z. H. Zhang*, Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/ Bcl-2 binding to Bad/Bax, : Phys. Chem. Chem. Phys., 2021, 23, 2025-203.
Guangfeng Shao, Jingxiao Bao, Xiaolin Pan, Xiao He*, Yifei Qi1* and John Z. H. Zhang*, Computational Analysis of Residue-Specific Binding Free Energies of Androgen Receptor to Ligands, Front. Mol. Biosci., 2021, 8, 646524.
Min Li*, John Zeng Hui Zhang, Multiscale polarizable coarse-graining water models on cluster-level electrostatic dipoles, Phys. Chem. Chem. Phys., 2021, 23, 8926-8935.
Song Luo, Kaifang Huang, Xiaoyu Zhao, Yalong Cong, John Z. H. Zhang and Lili Duan*, Inhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 Mpro by large-scale molecular dynamic simulations combined with accurate binding free energy calculations, Nanoscale, 2021, 13, 8313-8332.
Yao Liu, Yalong Cong, Chuanxi Zhang, Bohuan Fang, Yue Pan, Qiangzi Li, Chun You, Bei Gao, John Z. H. Zhang, Tong Zhu * and Lujia Zhang*, Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement, RSC Adv., 2021, 11, 12036-12042.
Xianwei Wang*, Jinhua Yan, Hang Zhang, Zhousu Xu, and John Z. H. Zhang*, An electrostatic energy-based charge model for molecular dynamics simulation, J. Chem. Phys., 2021, 154, 134107.
Junxiao Chen, Na Li, Xingyu Wang, Jianzhong Chen*, John Z. H. Zhang and Tong Zhu*, Molecular mechanism related to the binding of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations, Phys. Chem. Chem. Phys., 2021, 23, 10636-10649.
Ruiyao Chen, Yulu Miao, Xuan Hao, Bei Gao, Mingzhe Ma, John Z.H. Zhang, Rui Wang, Sha Li, Xiao He*, Lujia Zhang*, Investigation on the characteristics and mechanisms of ACE inhibitory peptides by a thorough analysis of all 8000 tripeptides via binding free energy calculation, Food Sci. Nutr., 2021, 9, 2943–2953.
Chih-Hao Chin*, Tong Zhu and John Zeng Hui Zhang*, Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: a theoretical study, Phys. Chem. Chem. Phys., 2021, 23, 12408-12420.
Guangfeng Shao, Jingxiao Bao, Xiaolin Pan, Xiao He*, Yifei Qi*, John Z.H. Zhang*, Analysis of the binding modes of the first- and second-generation antiandrogens with respect to F876L mutation, Chem. Biol. Drug. Des., 2021, 98, 60–72.
Jingxiao Bao, Xiao He,* and John Z. H. Zhang*, DeepBSPa Machine Learning Method for Accurate Prediction of Protein?Ligand Docking Structures, J. Chem. Inf. Model., 2021, 61, 2231?2240.
Zhendong Li and John Z. H. Zhang*, Quantitative analysis of ACE2 binding to coronavirus spike proteins: SARS-CoV-2 vs. SARS-CoV and RaTG13, Phys. Chem. Chem. Phys., 2021, 23, 13926.
Liqun Cao, Jinzhe Zeng , Mingyuan Xu, Chih-Hao Chin, Tong Zhu*, and John Z. H. Zhang*, Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion, Molecules, 2021, 26, 3120.
Xiaoyu Zhao, Song Luo, Kaifang Huang, Danyang Xiong, John Z. H. Zhang and Lili Duan *, Targeting mechanism for SARS-CoV-2 in silico: interaction and key groups of TMPRSS2 toward four potential drugs, Nanoscale, 2021, 13, 19218–19237.
Yue Zhao, Yulu Miao, Fengdong Zhi, Yue Pan, Jianguo Zhang, Xuepeng Yang, John Z. H. Zhang* and Lujia Zhang*, Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on Stability, Frontiers in Physics, 2021, 9, doi: 10.3389/fphy.2021.755253.
Xianwei Wang*, Xilong Li, Xiao He * and John Z. H. Zhang *, A fixed multi-site interaction charge model for an accurate prediction of the QM/MM interactions, Phys. Chem. Chem. Phys., 2021, 23, 21001–21012.
Wei Xia , Liping He , Jingxiao Bao , Yifei Qi* and John Z.H. Zhang*, Insights into small molecule inhibitor bindings to PD-L1 with residue-specific binding free energy calculation, Journal of Biomolecular Structure and Dynamics, 2021, DOI:10.1080/07391102.2021.1971558.
Lei Zheng, Yanmei Chen, Jingxiao Bao, Liping He, Suzhen Dong*, Yifei Qi* and John Z. H. Zhang*, Discovery of novel inhibitors of SARS-CoV-2 main protease, Journal of Biomolecular Structure and Dynamics, 2021, DOI:10.1080/07391102.2021.1972041.
Yuxi Lv, Song Luo, Kaifang Huang, Han Wang , Shuheng Dong, Yalong Cong, John Z.H. Zhang, Lili Duan*, Investigating effects of bridging water on the binding of neuraminidase-ligands using computational alanine scanning combined with interaction entropy method, Journal of Molecular Liquids, 2021, 336, 116214.
Yalong Cong, Yinghui Feng, Hui Ni, Fengdong Zhi, Yulu Miao, Bohuan Fang, Lujia Zhang,* and John Z. H. Zhang*, Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis, J. Chem. Inf. Model. 2021, 61, 3529?3542.
Xiaolin Pan, Hao Wang, Cuiyu Li, John Z. H. Zhang, and Changge Ji*, MolGpka: A Web Server for Small Molecule pK(a) Prediction Using a Graph-Convolutional Neural Network, J. Chem. Inf. Model. 2021, 61, 3159?3165.
WeiWen, DadingHuang, JingxiaoBao, John Z. H.Zhang*, Residue Specific Binding Mechanisms of PD-1 to Its Monoclonal Antibodies by Computational Alanine Scanning, Chemical Journal of Chinese Universities, 2021, 7, 2161-2169.
Wei Wen, Dading Huang, Jingxiao Bao and John Z.H. Zhang*, Residue-specific binding mechanisms of PD-L1 to its monoclonal antibodies by computational alanine scanning, Phys. Chem. Chem. Phys., 2021, 23, 15591–15600.
Mingyuan Xu, Tong Zhu*, and John Z. H. Zhang*, Automatically Constructed Neural Network Potentials for Molecular Dynamics Simulation of Zinc Proteins, Frontiers in Chemistry, 2021, 9, doi: 10.3389/fchem.2021.692200.
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