John Zhang

2014

Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin

Lin, B., Gao, Y., Li, Y., Zhang, J. Z. H. & Mei, Y., Apr 2014, In: Journal of Molecular Modeling. 20, 4, 2189.

Research output: Contribution to journal › Article › peer-review

Insights on Na⁺ binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM

Song, J., Ji, C. & Zhang, J. Z. H., Feb 2014, In: Proteins: Structure, Function and Bioinformatics. 82, 2, p. 240-249 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Molecular dynamics simulation of protein crystal with polarized protein-specific force field

Li, Y., Zhang, J. Z. H. & Mei, Y., Oct 30 2014, In: Journal of Physical Chemistry B. 118, 43, p. 12326-12335 10 p.

Research output: Contribution to journal › Article › peer-review

Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine

Liu, J., He, X. & Zhang, J. Z. H., Oct 1 2014, In: Journal of Molecular Modeling. 20, 10, 2451.

Research output: Contribution to journal › Article › peer-review

Protein's native structure is dynamically stabilized by electronic polarization

Duan, L. L., Mei, Y., Zhang, Q. G., Tang, B. & Zhang, J. Z. H., May 2014, In: Journal of Theoretical and Computational Chemistry. 13, 3, 1440005.

Research output: Contribution to journal › Article › peer-review

Structure, mechanism, and enantioselectivity shifting of lipase LipK107 with a simple way

Zhang, L., Gao, B., Yuan, Z., He, X., Adam Yuan, Y., Zhang, J. Z. H. & Wei, D., Jul 2014, In: Biochimica et Biophysica Acta - Proteins and Proteomics. 1844, 7, p. 1183-1192 10 p.

Research output: Contribution to journal › Article › peer-review

Time-dependent treatment of SVRT model for polyatom-polyatom reaction

Zhang, J. Z. H., 2014, Reaction Rate Constant Computations. Han, K. & Chu, T. (eds.). p. 337-351 15 p. (RSC Theoretical and Computational Chemistry Series).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

2013

Acidic pH retards the fibrillization of human islet amyloid polypeptide due to electrostatic repulsion of histidines

Li, Y., Xu, W., Mu, Y. & Zhang, J. Z. H., Aug 7 2013, In: Journal of Chemical Physics. 139, 5, 055102.

Research output: Contribution to journal › Article › peer-review

A coupled two-dimensional main chain torsional potential for protein dynamics: Generation and implementation

Li, Y., Gao, Y., Zhang, X., Wang, X., Mou, L., Duan, L., He, X., Mei, Y. & Zhang, J. Z. H., Sep 2013, In: Journal of Molecular Modeling. 19, 9, p. 3647-3657 11 p.

Research output: Contribution to journal › Article › peer-review

A new quantum calibrated force field for zinc-protein complex

Zhu, T., Xiao, X., Ji, C. & Zhang, J. Z. H., Mar 12 2013, In: Journal of chemical theory and computation. 9, 3, p. 1788-1798 11 p.

Research output: Contribution to journal › Article › peer-review

An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins

Duan, L. L., Zhu, T., Mei, Y., Zhang, Q. G., Tang, B. & Zhang, J. Z. H., Jun 2013, In: Journal of Molecular Modeling. 19, 6, p. 2605-2612 8 p.

Research output: Contribution to journal › Article › peer-review

An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins

Jia, X., Wang, X., Liu, J., Zhang, J. Z. H., Mei, Y. & He, X., Dec 7 2013, In: Journal of Chemical Physics. 139, 21, 214104.

Research output: Contribution to journal › Article › peer-review

A numerically stable restrained electrostatic potential charge fitting method

Zeng, J., Duan, L., Zhang, J. Z. H. & Mei, Y., Apr 5 2013, In: Journal of Computational Chemistry. 34, 10, p. 847-853 7 p.

Research output: Contribution to journal › Article › peer-review

Assessing the accuracy of the general AMBER force field for 2,2,2-trifluoroethanol as solvent

Jia, X., Zhang, J. Z. H. & Mei, Y., Jun 2013, In: Journal of Molecular Modeling. 19, 6, p. 2355-2361 7 p.

Research output: Contribution to journal › Article › peer-review

Automated fragmentation QM/MM calculation of amide proton chemical shifts in proteins with explicit solvent model

Zhu, T., Zhang, J. Z. H. & He, X., Apr 9 2013, In: Journal of chemical theory and computation. 9, 4, p. 2104-2114 11 p.

Research output: Contribution to journal › Article › peer-review

Computational study of hiv-1 gp41 nhr trimer: Inhibition mechanisms of n-substituted pyrrole derivatives and fragment-based virtual screening

Bao, J., Liu, J. F., He, X. & Zhang, J. Z. H., Dec 2013, In: Journal of Theoretical and Computational Chemistry. 12, 8, 1341001.

Research output: Contribution to journal › Article › peer-review

Development of an effective polarizable bond method for biomolecular simulation

Xiao, X., Zhu, T., Ji, C. G. & Zhang, J. Z. H., Dec 5 2013, In: Journal of Physical Chemistry B. 117, 48, p. 14885-14893 9 p.

Research output: Contribution to journal › Article › peer-review

Direct folding simulation of a long helix in explicit water

Gao, Y., Lu, X., Duan, L., Zhang, D., Mei, Y. & Zhang, J. Z. H., May 13 2013, In: Applied Physics Letters. 102, 19, 193706.

Research output: Contribution to journal › Article › peer-review

Open Access

Discovery and characterization of novel, potent, and selective cytochrome P450 2J2 inhibitors

Ren, S., Zeng, J., Mei, Y., Zhang, J. Z. H., Yan, S. F., Fei, J. & Chen, L., Jan 2013, In: Drug Metabolism and Disposition. 41, 1, p. 60-71 12 p.

Research output: Contribution to journal › Article › peer-review

Effect of self-assembly of fullerene nano-particles on lipid membrane.

Zhang, S., Mu, Y., Zhang, J. Z. H. & Xu, W., 2013, In: PloS one. 8, 10

Research output: Contribution to journal › Article › peer-review

Open Access

Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy

Wang, X., Liu, J., Zhang, J. Z. H. & He, X., Aug 15 2013, In: Journal of Physical Chemistry A. 117, 32, p. 7149-7161 13 p.

Research output: Contribution to journal › Article › peer-review

Hybrid many-body-expansion/Shepard-interpolation method for constructing ab initio potential energy surfaces for quantum dynamics calculations

Lin, S. Y., Zhang, P. & Zhang, J. Z. H., Jan 29 2013, In: Chemical Physics Letters. 556, p. 393-397 5 p.

Research output: Contribution to journal › Article › peer-review

Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization

Liu, J., He, X. & Zhang, J. Z. H., Jun 24 2013, In: Journal of Chemical Information and Modeling. 53, 6, p. 1306-1314 9 p.

Research output: Contribution to journal › Article › peer-review

Interaction specific binding hotspots in Endonuclease colicin-immunity protein complex from MD simulations

Yao, X., Ji, C., Xie, D. & Zhang, J. Z. H., Aug 2013, In: Science China Chemistry. 56, 8, p. 1143-1151 9 p.

Research output: Contribution to journal › Article › peer-review

Molecular dynamics simulation and computational two-dimensional infrared spectroscopic study of model amyloid β-peptide oligomers

Xu, J., Zhang, J. Z. H. & Xiang, Y., Jul 25 2013, In: Journal of Physical Chemistry A. 117, 29, p. 6373-6379 7 p.

Research output: Contribution to journal › Article › peer-review

Molecular dynamics study of DNA binding by INT-DBD under a polarized force field

Yao, X. X., Ji, C. G., Xie, D. Q. & Zhang, J. Z. H., May 15 2013, In: Journal of Computational Chemistry. 34, 13, p. 1136-1142 7 p.

Research output: Contribution to journal › Article › peer-review

PH-dependent conformational ensemble and polymorphism of amyloid-β core fragment

Xu, W., Zhang, C., Morozova-Roche, L., Zhang, J. Z. H. & Mu, Y., Jul 18 2013, In: Journal of Physical Chemistry B. 117, 28, p. 8392-8399 8 p.

Research output: Contribution to journal › Article › peer-review

Predicting mutation-induced stark shifts in the active site of a protein with a polarized force field

Wang, X., He, X. & Zhang, J. Z. H., Jul 25 2013, In: Journal of Physical Chemistry A. 117, 29, p. 6015-6023 9 p.

Research output: Contribution to journal › Article › peer-review

The critical effect of polarization on the dynamical structure of guanine quadruplex DNA

Song, J., Ji, C. & Zhang, J. Z. H., Mar 21 2013, In: Physical Chemistry Chemical Physics. 15, 11, p. 3846-3854 9 p.

Research output: Contribution to journal › Article › peer-review

The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect

Zeng, J., Jia, X., Zhang, J. Z. H. & Mei, Y., Dec 5 2013, In: Journal of Computational Chemistry. 34, 31, p. 2677-2686 10 p.

Research output: Contribution to journal › Article › peer-review

The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: A replica exchange molecular dynamics study

Lu, X., Zeng, J., Gao, Y., Zhang, J. Z. H., Zhang, D. & Mei, Y., Nov 2013, In: Journal of Molecular Modeling. 19, 11, p. 4897-4908 12 p.

Research output: Contribution to journal › Article › peer-review

Unveiling the gating mechanism of ecf transporter ribu

Song, J., Ji, C. & Zhang, J. Z. H., Dec 20 2013, In: Scientific reports. 3, 3566.

Research output: Contribution to journal › Article › peer-review

2012

Ab initio QM/MM free energy simulations of peptide bond formation in the ribosome support an eight-membered ring reaction mechanism

Xu, J., Zhang, J. Z. H. & Xiang, Y., Oct 3 2012, In: Journal of the American Chemical Society. 134, 39, p. 16424-16429 6 p.

Research output: Contribution to journal › Article › peer-review

A fragmentation approach to quantum calculation of large molecular systems

Mei, Y., He, X., Ji, C., Zhang, D. & Zhang, J. Z. H., Jun 2012, In: Progress in Chemistry. 24, 6, p. 1058-1064 7 p.

Research output: Contribution to journal › Article › peer-review

Calculation of collective variable-based PMF by combining WHAM with umbrella sampling

Xu, W. X., Li, Y. & Zhang, J. Z. H., Jun 2012, In: Chinese Physics Letters. 29, 6, 068702.

Research output: Contribution to journal › Article › peer-review

Combined theoretical and experimental study on high diastereoselective chirality transfer based on [2.2]paracyclophane derivative chiral reagent

Jiang, B., Han, L., Li, Y. L., Zhao, X. L., Lei, Y., Xie, D. Q. & Zhang, J. Z. H., Feb 17 2012, In: Journal of Organic Chemistry. 77, 4, p. 1701-1709 9 p.

Research output: Contribution to journal › Article › peer-review

Dynamical stability and assembly cooperativity of β-sheet amyloid oligomers - Effect of polarization

Li, Y., Ji, C., Xu, W. & Zhang, J. Z. H., Nov 15 2012, In: Journal of Physical Chemistry B. 116, 45, p. 13368-13373 6 p.

Research output: Contribution to journal › Article › peer-review

Effect of interprotein polarization on protein-protein binding energy

Ji, C. G. & Zhang, J. Z. H., Jun 15 2012, In: Journal of Computational Chemistry. 33, 16, p. 1416-1420 5 p.

Research output: Contribution to journal › Article › peer-review

Electrostatic polarization is critical for the strong binding in streptavidin-biotin system

Mei, Y., Li, Y. L., Zeng, J. & Zhang, J. Z. H., Jun 5 2012, In: Journal of Computational Chemistry. 33, 15, p. 1374-1382 9 p.

Research output: Contribution to journal › Article › peer-review

Exploring the molecular mechanism of stabilization of the adhesion domains of human CD2 by N-glycosylation

Wang, X. Y., Ji, C. G. & Zhang, J. Z. H., Sep 27 2012, In: Journal of Physical Chemistry B. 116, 38, p. 11570-11577 8 p.

Research output: Contribution to journal › Article › peer-review

Folding and thermodynamic studies of Trp-cage based on polarized force field

Mei, Y., Wei, C., Yip, Y. M., Ho, C. Y., Zhang, J. Z. H. & Zhang, D., Mar 2012, In: Theoretical Chemistry Accounts. 131, 3, p. 1-7 7 p., 1168.

Research output: Contribution to journal › Letter › peer-review

Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: Study in explicit water

Duan, L. L., Gao, Y., Mei, Y., Zhang, Q. G., Tang, B. & Zhang, J. Z. H., Mar 15 2012, In: Journal of Physical Chemistry B. 116, 10, p. 3430-3435 6 p.

Research output: Contribution to journal › Article › peer-review

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

Zhu, T., He, X. & Zhang, J. Z. H., Jun 7 2012, In: Physical Chemistry Chemical Physics. 14, 21, p. 7837-7845 9 p.

Research output: Contribution to journal › Article › peer-review

Molecular dynamics simulation study on the molecular structures of the amylin fibril models

Xu, W., Su, H., Zhang, J. Z. H. & Mu, Y., Dec 6 2012, In: Journal of Physical Chemistry B. 116, 48, p. 13991-13999 9 p.

Research output: Contribution to journal › Article › peer-review

Polarization of intraprotein hydrogen bond is critical to thermal stability of short helix

Gao, Y., Lu, X., Duan, L. L., Zhang, J. Z. H. & Mei, Y., Jan 12 2012, In: Journal of Physical Chemistry B. 116, 1, p. 549-554 6 p.

Research output: Contribution to journal › Article › peer-review

Protein-water hydrogen bonds are stabilized by electrostatic polarization

Gao, Y., Guo, M., Mei, Y. & Zhang, J. Z. H., May 10 2012, In: Molecular Physics. 110, 9-10, p. 595-604 10 p.

Research output: Contribution to journal › Article › peer-review

Studying the effect of site-specific hydrophobicity and polarization on hydrogen bond energy of protein using a polarizable method

Ji, C. G., Xiao, X. & Zhang, J. Z. H., Jun 12 2012, In: Journal of chemical theory and computation. 8, 6, p. 2157-2164 8 p.

Research output: Contribution to journal › Article › peer-review

2011

Computational characterization of binding of small molecule inhibitors to HIV-1 gp41

Song, K., Bao, J., Sun, Y. & Zhang, J. Z. H., Jul 2011, In: Chinese Journal of Chemistry. 29, 7, p. 1307-1311 5 p.

Research output: Contribution to journal › Article › peer-review

Effect of polarization on the stability of a helix dimer

Wang, X. Y. & Zhang, J. Z. H., Jan 7 2011, In: Chemical Physics Letters. 501, 4-6, p. 508-512 5 p.

Research output: Contribution to journal › Article › peer-review

Folding of EK peptide and its dependence on salt concentration and pH: A computational study

Mei, Y., Zhang, D., Duan, L., Zhang, Q. & Zhang, J. Z., Dec 2011, In: Science China Chemistry. 54, 12, p. 1974-1981 8 p.

Research output: Contribution to journal › Article › peer-review

John Zhang

Research output

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