55. Zeng, J. Z.; Cao, L. Q.; Xu, M. Y.; Zhu T.*; Zhang, J. Z. H.*, Neural Network Based in Silico Simulation of Combustion Reactions. arXiv:1911.12252.

54. Zeng, J. Z.,‡ Cao, L. Q., ‡ Chin, C. H.;* Ren, H. S.;* Zhang, J. Z. H.; Zhu T.*, ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations. Phys. Chem. Chem. Phys., 2020, 22, 683-691.Graphical abstract: ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations



53. Chin, C. H.*; Zhu T.*; Zhang J. Z. H., Formation mechanism and spectroscopy of C6H radicals in extreme environments: a theoretical study. Phys. Chem. Chem. Phys., 2019, 21, 23044-23055

52. Tian, S. Z.; Zeng, J. Z.; Liu, X.*; Chen, J. Z.; Zhang, J. Z. H.; Zhu T.*, Understanding the selectivity of inhibitiors toward PI4KIIIa and PI4KIIIb based molecular modeling. Phys. Chem. Chem. Phys., 2019, 21, 22103-22112

51. Chen, J. Z.*; Pang, L. X.; Wang, W.; Wang, L. F.; Zhang, J. Z. H.; Zhu T.*, Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies.  J. Biomol. Struct. Dyn., 2019, 21, 22103-22112J. Biomol. Struct. Dyn., 2019, DOI: 10.1080/07391102.2019.1624616.

50. Xu, M.Y.; Zhu T.*; Zhang J.Z.H.*, Molecular Dynamics Simulation of Zinc Ion in Water with an Ab Initio Based Neural Network Potential. J. Phys. Chem. A. 2019, 123, 6587-6595.

49. Tang, Q.; Plank, T. N.; Zhu T.; Yu H. Z.; Ge Z. L.; Li Q.; Li L.; Davis J. T.*; Pei H.*, Self-Assembly of Metallo-Nucleoside Hydrogels for Injectable Materials That Promote Wound Closure. ACS Appl. Mater. Interfaces. 2019, 11, 19743−19750

48. Zhao, P.; Han, S.; Li, X. X.*; Zhu T.*; Tao, X. F.; Guo, L., Comparison of RP-3 Pyrolysis Reactions Between Surrogates and 45-component Model by ReaxFF MD Simulations. ACS Energy Fuels. 2019, 33, 7176-7187.

47. Sun, Z. X.*; Wang, X. H.; Zhao, Q. Q.; Zhu, T., Understanding Aldose Reductase-Inhibitors interactions with free energy simulation.  J. Mol. Graph. Model., 2019, 91, 10-21. 

46. Chen, J. Z.*; Wang, X. Y.; Pang, L. X.; Zhang, J. Z. H.; Zhu T.*, Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations. Nucleic Acids Res. 2019, 47, 6618-6631.

45. Zhao, P.; Cao, H. L.; Chen, Y.; Zhu T.*, Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations. Chem. Phys. Lett., 2019, 728, 94-101.

44. Chen, J. Z.*; Pang, L. X.; Wang, W.; Wang, L. F.; Zhang, J. Z. H.; Zhu T.*, Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations. J. Biomol. Struct. Dyn., 2019, 8, 1-12.

43. Zhu, M. F.; Wang H.; Wang C. L.; Fang Y. F.; Zhu T.; Zhao W. L.; Dong X. C.*; Zhang X. W.*, L-4, a Well-Tolerated and Orally Active Inhibitor of Hedgehog Pathway, Exhibited Potent Anti-tumor Effects Against Medulloblastoma in vitro and in vivo. Front. Pharm. 2019, 10, 1-13.

42. Xu, M. Y.; Zhu T.*; Zhang, J. Z. H.*, A Fragment Quantum Mechanical Method for Metalloproteins. J. Chem. Theory Comput., 2019, 15, 1430–1439.


41. Chen, J. Z.*; Wang, X. Y.; Zhang, J. Z. H.; Zhu T.*, Effect of Substituents in Different Positions of Aminothiazole Hinge-Binding Scaffolds on Inhibitor–CDK2 Association Probed by Interaction Entropy Method. ACS Omega, 2018, 3, 18052–18064.

40. Gao, Y.; Zhu T.*; Zhang, C. M.; Zhang, J. Z. H.; Mei, Y.*, Comparison of the Unfolding and Oligomerization of Human Prion Protein under acidic and neutral environments by Molecular Dynamics Simulations. Chem. Phys. Lett. 2018, 706, 594-600.

39. Gao, Y.; Zhu, T.*; Chen, J. Z.*, Exploring Drug-resistant Mechanisms of I84V Mutation in HIV-1 Protease toward Different Inhibitors by Thermodynamics Integration and Solvated Interaction Energy Method. Chem. Phys. Lett. 2018, 706, 400-408.

38. Yang, Q.; Hu, Z.; Zhu, S.; Ma, R.; Ma, H.; Ma, Z.; Wan, H.; Zhu, T.; Jiang, Z.; Liu, W.; Jiao, L.; Sun, H.; Liang, Y.; Dai, H., Donor Engineering for NIR-II Molecular Fluorophores with Enhanced Fluorescent Performance. J. Am. Chem. Soc. 2018, 140, 1715-1724.

37. Xu, M.; Zhu, T.*; Zhang, J. Z. H.*, A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein. Front. Chem. 2018, 6, 189.

36. Wang, X.*; Li, Y.; Gao, Y.; Yang, Z.; Lu, C.; Zhu, T.*, A quantum mechanical computational method for modeling electrostatic and solvation effects of protein. Sci. Rep. 2018, 8, 5475.

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


34. Xi, J.-B.; Fang, Y.-F.; Frett, B.; Zhu, M.-L.; Zhu, T.; Kong, Y.-N.; Guan, F.-J.; Zhao, Y.; Zhang, X.-W.; Li, H.-Y.; Ma, M.-L.; Hu, W., Structure-based design and synthesis of imidazo 1,2-a pyridine derivatives as novel and potent Nek2 inhibitors with in vitro and in vivo antitumor activities. Eur. J. Med. Chem. 2017, 126, 1083-1106.

33. Sun, Z.; Zhu, T.; Wang, X.; Mei, Y.; Zhang, J. Z. H., Optimization of convergence criteria for fragmentation methods. Chem. Phys. Lett. 2017, 687, 163-170.

32. Luo, Z.; Gao, Y.; Zhu, T.*; Zhang, J. Z.; Xia, F.*, Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules. J. Phys. Chem. A 2017, 121, 6523-6529.

31. Liu, L.; Zhao, F.; Liu, W.; Zhu, T.; Zhang, J. Z. H.; Chen, C.; Dai, Z.; Peng, H.; Huang, J.-L.; Hu, Q.; Bu, W.; Tian, Y., An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O-2 in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy. Angew. Chem. Int. Edit. 2017, 56, 10471-10475.

30. Li, S.; Zhu, A.; Zhu, T.; Zhang, J. Z. H.; Tian, Y., Single Biosensor for Simultaneous Quantification of Glucose and pH in a Rat Brain of Diabetic Model Using Both Current and Potential Outputs. Anal. Chem. 2017, 89, 6656-6662.

29. Jing, C.; Li, Z.; Jia, K.; Chen, C.; Liu, X.; Wang, B.; Hu, W.; Li, J.; Zhu, T*.; Dong, S.*, Discovery of Bisindole as a Novel Scaffold for Protein Tyrosine Phosphatase 1B Inhibitors. Arch. Pharm. 2017, 350, e1600173.

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

27. Gao, Y.; Zhang, C.; Wang, X.; Zhu, T.*, A test of AMBER force fields in predicting the secondary structure of alpha-helical and beta-hairpin peptides. Chem. Phys. Lett. 2017, 679, 112-118.

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

25. Duan, L.; Zhu, T.; Ji, C.; Zhang, Q.; Zhang, J. Z. H., Direct folding simulation of helical proteins using an effective polarizable bond force field. Phys. Chem. Chem. Phys. 2017, 19, 15273-15284.

24. Dong, S.; Lei, Y.; Jia, S.; Gao, L.; Li, J.; Zhu, T.; Liu, S.; Hu, W., Discovery of core-structurally novel PTP1B inhibitors with specific selectivity containing oxindole-fused spirotetrahydrofurochroman by one-pot reaction. Bioorg. Med. Chem. Lett. 2017, 27, 1105-1108.


23. Wang, Y.; Liu, J. F.; Zhu, T.; Zhang, L. J.; He, X.; Zhang, J. Z. H., Predicted PAR1 inhibitors from multiple computational methods. Chem. Phys. Lett. 2016, 659, 295-303.

22. Lv, F.; Chen, C.; Tang, Y.; Wei, J.; Zhu, T.*; Hu, W*., New peptide deformylase inhibitors design, synthesis and pharmacokinetic assessment. Bioorg. Med. Chem. Lett.  2016, 26, 3714-3718.

21. Liu, X.; Liu, J. F.; Zhu, T.; Zhang, L. J.; He, X.; Zhang, J. Z. H., PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity. J. Chem. Inf. Model. 2016, 56, 854-861.

20. Liu, W.; Lu, Y.; Chai, X.; Liu, X.; Zhu, T.; Wu, X.; Fang, Y.; Liu, X.; Zhang, X.*, Antitumor activity of TY-011 against gastric cancer by inhibiting Aurora A, Aurora B and VEGFR2 kinases. J. Exp. Clin. Canc. Res. 2016, 35, 183.

19. Jin, X.; Zhu, T.; Zhang, J. Z. H.; He, X.*, A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach. RSC Adv. 2016, 6, 108590-108602.

18. Fang, Y.; Kong, Y.; Xi, J.; Zhu, M.; Zhu, T.; Jiang, T.; Hu, W.; Ma, M.*; Zhang, X.*, Preclinical activity of MBM-5 in gastrointestinal cancer by inhibiting NEK2 kinase activity. Oncotarget 2016, 7, 79313-79327.


17. Zhu, T.; Zhang, J. Z. H.*; He, X.*, Quantum Calculation of Protein NMR Chemical Shifts Based on the Automated Fragmentation Method. In Advance in Structural Bioinformatics, Wei, D.; Xu, Q.; Zhao, T.; Dai, H., Eds. 2015; Vol. 827, pp 49-70.

16. Swails, J.; Zhu, T.; He, X.*; Case, D. A.*, AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J. Biomol. NMR  2015, 63, 125-139.

15. Liu, J.; Zhu, T*.; Wang, X.; He, X.*; Zhang, J. Z. H*., Quantum Fragment Based ab Initio Molecular Dynamics for Proteins. J. Chem. Theory Comput. 2015, 11, 5897-5905.

14. Chen, J.; Wang, X.; Zhu, T.*; Zhang, Q.; Zhang, J. Z. H., 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. 2015, 55, 1903-1913.


13. Zhu, T.; Zhang, J. Z. H.; He, X.*, Correction of erroneously packed protein’s side chains in the NMR structure based on ab initio chemical shift calculations. Phys. Chem. Chem. Phys. 2014, 16, 18163-18169.

12. He, X.*; Zhu, T.; Wang, X.; Liu, J.; Zhang, J. Z. H.*, Fragment Quantum Mechanical Calculation of Proteins and Its Applications. Accounts Chem. Res. 2014, 47, 2748-2757.

11. Duan, L. L.; Zhu, T.; Zhang, Q. G.; Tang, B.*; Zhang, J. Z. H.*, Electronic polarization stabilizes tertiary structure prediction of HP-36. J. Mol. Model. 2014, 20.

10. Chen, J.; Chen, H.; Zhu, T.; Zhou, D.; Zhang, F.; Lao, X.*; Zheng, H.*, Asp120Asn mutation impairs the catalytic activity of NDM-1 metallo-beta-lactamase: experimental and computational study. Phys. Chem. Chem. Phys. 2014, 16, 6709-6716.

9. Zhu, T.; Zhang, J. Z. H.; He, X.*, Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model.  J. Chem. Theory Comput. 2013, 9, 2104-2114.

8. Zhu, T.; Xiao, X.; Ji, C.*; Zhang, J. Z. H.*, A New Quantum Calibrated Force Field for Zinc-Protein Complex.  J. Chem. Theory Comput. 2013, 9, 1788-1798.

7. 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. 2013, 19, 2605-2612.

6. Zhu, T.; He, X.*; Zhang, J. Z. H., Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Phys. Chem. Chem. Phys. 2012, 14, 7837-7845.

5. Zhu, T.; Hu, G. D.; Zhang, Q. G.*, Quasi-classical Trajectory Study of Reaction O (P-3) plus HCl (v=2; j=1, 6, 9) -> OH plus Cl. Chinese Phys. Lett. 2010, 27.

4. Zhu, T.; Hu, G.-D.; Chen, J. Z.; Liu, X. G.; Zhang, Q. G., Theoretical study of stereodynamics for reaction O(P-3)+HCl. Chinese Phys. B 2010, 19.

3. Zhu, T.; Hu, G.; Zhang, Q.*, Quasi-classical trajectory study of the reaction O(P-3) plus HCl -> OH + Cl and O(P-3) plus DCl -> OD plus Cl: Vector and scalar properties. J. Mol. Struc-Theochem 2010, 948, 36-42.

2. Liu, H.; Liu, X.; Zhu, T.; Sun, H.; Zhang, Q.*, THE EFFECT OF VIBRATIONAL EXCITATION OF THE REACTION O(P-3)+HCl -> OH plus Cl FOR THE (3)A ” ELECTRONIC STATES. J. Theor. Comput. Chem. 2010, 9, 1033-1042.

1. Hu, G.-D.; Zhu, T.; Zhang, S.-L.; Wang, D.; Zhang, Q.-G.*, Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations. Eur. J. Med. Chem. 2010, 45, 227-235.50