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Tong Zhu, Ph.D. - Publications

Affiliations: 
2003-2010 Shandong Normal University 
 2010- School of Chemistry and Molecular Engineering East China Normal University, Shanghai, Shanghai Shi, China 
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41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Cao L, Zeng J, Wang B, Zhu T, Zhang JZH. neural network MD simulation of thermal decomposition of a high energy material CL-20/TNT. Physical Chemistry Chemical Physics : Pccp. PMID 35506927 DOI: 10.1039/d2cp00710j  0.601
2021 Cao L, Zeng J, Xu M, Chin CH, Zhu T, Zhang JZH. Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion. Molecules (Basel, Switzerland). 26. PMID 34071128 DOI: 10.3390/molecules26113120  0.633
2021 Chen J, Li N, Wang X, Chen J, Zhang JZH, Zhu T. Molecular mechanism related to the binding of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations. Physical Chemistry Chemical Physics : Pccp. PMID 33904542 DOI: 10.1039/d0cp06438f  0.431
2020 Zeng J, Cao L, Xu M, Zhu T, Zhang JZH. Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation. Nature Communications. 11: 5713. PMID 33177517 DOI: 10.1038/s41467-020-19497-z  0.59
2020 Wang B, Li C, Xiangyu J, Zhu T, Zhang JZH. An Approach to Computing Solvent Reorganization Energy. Journal of Chemical Theory and Computation. PMID 32941037 DOI: 10.1021/Acs.Jctc.0C00672  0.375
2020 Li C, Chin C, Zhu T, Hui Zhang JZ. An ab initio/RRKM study of the reaction mechanism and product branching ratios of CH3OH+ and CH3OH++ dissociation Journal of Molecular Structure. 1217: 128410. DOI: 10.1016/J.Molstruc.2020.128410  0.34
2020 Gao Z, Bao J, Shi S, Zhang X, Gao Y, Zhu T. Effect of mutations on drug resistance of smoothened receptor toward inhibitors probed by molecular modeling Chemical Physics Letters. 741: 137126. DOI: 10.1016/J.Cplett.2020.137126  0.315
2019 Zeng J, Cao L, Chin CH, Ren H, Zhang JZH, Zhu T. ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations. Physical Chemistry Chemical Physics : Pccp. PMID 31829361 DOI: 10.1039/C9Cp05091D  0.613
2019 Chin CH, Zhu T, Zhang JZH. Formation mechanism and spectroscopy of CH radicals in extreme environments: a theoretical study. Physical Chemistry Chemical Physics : Pccp. PMID 31599891 DOI: 10.1039/C9Cp03662H  0.319
2019 Tian S, Zeng J, Liu X, Chen J, Zhang JZH, Zhu T. Understanding the selectivity of inhibitors toward PI4KIIIα and PI4KIIIβ based molecular modeling. Physical Chemistry Chemical Physics : Pccp. PMID 31570909 DOI: 10.1039/C9Cp03598B  0.629
2019 Xu M, Zhu T, Zhang JZH. Molecular Dynamics Simulation of Zinc Ion in Water with an Ab Initio Based Neural Network Potential. The Journal of Physical Chemistry. A. PMID 31294560 DOI: 10.1021/Acs.Jpca.9B04087  0.359
2019 Chen J, Yin B, Pang L, Wang W, Zhang JZH, 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. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 31198099 DOI: 10.1080/07391102.2019.1624616  0.359
2019 Chen J, Wang X, Pang L, Zhang JZH, Zhu T. Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations. Nucleic Acids Research. PMID 31173143 DOI: 10.1093/Nar/Gkz499  0.539
2019 Sun Z, Wang X, Zhao Q, Zhu T. Understanding Aldose Reductase-Inhibitors interactions with free energy simulation. Journal of Molecular Graphics & Modelling. 91: 10-21. PMID 31128525 DOI: 10.1016/J.Jmgm.2019.05.011  0.74
2019 Chen J, Pang L, Wang W, Wang L, Zhang JZH, Zhu T. Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations. Journal of Biomolecular Structure & Dynamics. 1-23. PMID 30843759 DOI: 10.1080/07391102.2019.1591304  0.393
2019 Xu M, He X, Zhu T, Zhang JZH. A Fragment Quantum Mechanical Method for Metalloproteins. Journal of Chemical Theory and Computation. PMID 30620584 DOI: 10.1021/Acs.Jctc.8B00966  0.414
2019 Zhao P, Cao H, Chen Y, Zhu T. Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations Chemical Physics Letters. 728: 94-101. DOI: 10.1016/J.Cplett.2019.05.001  0.402
2018 Xu M, Zhu T, Zhang JZH. A Force Balanced Fragmentation Method for Molecular Dynamic Simulation of Protein. Frontiers in Chemistry. 6: 189. PMID 29900167 DOI: 10.3389/Fchem.2018.00189  0.382
2018 Jin X, Zhu T, Zhang JZH, He X. Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes. Frontiers in Chemistry. 6: 150. PMID 29868556 DOI: 10.3389/Fchem.2018.00150  0.378
2018 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. Scientific Reports. 8: 5475. PMID 29615707 DOI: 10.1038/S41598-018-23783-8  0.376
2018 Gao Y, Zhu T, Zhang C, Zhang JZ, Mei Y. Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations Chemical Physics Letters. 706: 594-600. DOI: 10.1016/J.Cplett.2018.07.014  0.325
2018 Gao Y, Zhu T, Chen J. Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method Chemical Physics Letters. 706: 400-408. DOI: 10.1016/J.Cplett.2018.06.040  0.333
2017 Duan L, Zhu T, Ji C, Zhang Q, Zhang JZH. Direct folding simulation of helical proteins using an effective polarizable bond force field. Physical Chemistry Chemical Physics : Pccp. PMID 28569909 DOI: 10.1039/C7Cp02101A  0.346
2017 Duan LL, Zhu T, Li YC, Zhang QG, Zhang JZ. Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations. Scientific Reports. 7: 42223. PMID 28155907 DOI: 10.1038/Srep42223  0.403
2017 Sun Z, Zhu T, Wang X, Mei Y, Zhang JZ. Optimization of convergence criteria for fragmentation methods Chemical Physics Letters. 687: 163-170. DOI: 10.1016/J.Cplett.2017.08.059  0.722
2016 Liu X, Liu J, Zhu T, Zhang L, He X, Zhang JZ. PBSA_E: A PBSA based free energy estimator for protein-ligand binding affinity. Journal of Chemical Information and Modeling. PMID 27088302 DOI: 10.1021/Acs.Jcim.6B00001  0.353
2016 Jin X, Zhu T, Zhang JZH, He X. A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach Rsc Advances. 6: 108590-108602. DOI: 10.1039/C6Ra22518G  0.305
2016 Wang Y, Liu J, Zhu T, Zhang L, He X, Zhang JZH. Predicted PAR1 inhibitors from multiple computational methods Chemical Physics Letters. 659: 295-303. DOI: 10.1016/J.Cplett.2016.07.059  0.405
2015 Liu J, Zhu T, Wang X, He X, Zhang JZ. Quantum Fragment Based ab Initio Molecular Dynamics for Proteins. Journal of Chemical Theory and Computation. 11: 5897-5905. PMID 26642993 DOI: 10.1021/Acs.Jctc.5B00558  0.406
2015 Chen J, Wang X, Zhu T, Zhang Q, Zhang JZ. 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. Journal of Chemical Information and Modeling. PMID 26317593 DOI: 10.1021/Acs.Jcim.5B00173  0.504
2015 Swails J, Zhu T, He X, Case DA. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. Journal of Biomolecular Nmr. 63: 125-39. PMID 26232926 DOI: 10.1007/S10858-015-9970-3  0.329
2015 Zhu T, Zhang JZ, He X. Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method. Advances in Experimental Medicine and Biology. 827: 49-70. PMID 25387959 DOI: 10.1007/978-94-017-9245-5_5  0.368
2014 Zhu T, Zhang JZ, He X. Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations. Physical Chemistry Chemical Physics : Pccp. 16: 18163-9. PMID 25052367 DOI: 10.1039/C4Cp02553A  0.341
2014 He X, Zhu T, Wang X, Liu J, Zhang JZ. Fragment quantum mechanical calculation of proteins and its applications. Accounts of Chemical Research. 47: 2748-57. PMID 24851673 DOI: 10.1021/Ar500077T  0.41
2014 Duan LL, Zhu T, Zhang QG, Tang B, Zhang JZ. Electronic polarization stabilizes tertiary structure prediction of HP-36. Journal of Molecular Modeling. 20: 2195. PMID 24715046 DOI: 10.1007/S00894-014-2195-7  0.343
2013 Zhu T, Xiao X, Ji C, Zhang JZ. A New Quantum Calibrated Force Field for Zinc-Protein Complex. Journal of Chemical Theory and Computation. 9: 1788-98. PMID 26587635 DOI: 10.1021/Ct301091Z  0.367
2013 Zhu T, Zhang JZ, He X. Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model. Journal of Chemical Theory and Computation. 9: 2104-14. PMID 26583557 DOI: 10.1021/Ct300999W  0.348
2013 Xiao X, Zhu T, Ji CG, Zhang JZ. Development of an effective polarizable bond method for biomolecular simulation. The Journal of Physical Chemistry. B. 117: 14885-93. PMID 24251550 DOI: 10.1021/Jp4080866  0.378
2013 Duan LL, Zhu T, Mei Y, Zhang QG, Tang B, Zhang JZ. An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins. Journal of Molecular Modeling. 19: 2605-12. PMID 23479281 DOI: 10.1007/S00894-013-1798-8  0.349
2012 Zhu T, He X, Zhang JZ. Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Physical Chemistry Chemical Physics : Pccp. 14: 7837-45. PMID 22314755 DOI: 10.1039/C2Cp23746F  0.35
2010 Hu GD, Zhu T, Zhang SL, Wang D, Zhang QG. 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. European Journal of Medicinal Chemistry. 45: 227-35. PMID 19910081 DOI: 10.1016/J.Ejmech.2009.09.048  0.634
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