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 |
0.634 |
|
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 |
0.435 |
|
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 |
0.377 |
|
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 |
0.341 |
|
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 |
0.316 |
|
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 |
0.32 |
|
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 |
0.63 |
|
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 |
0.36 |
|
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 |
0.361 |
|
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 |
0.543 |
|
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 |
0.738 |
|
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 |
0.395 |
|
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 |
0.417 |
|
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 |
0.404 |
|
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 |
0.384 |
|
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 |
0.379 |
|
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 |
0.378 |
|
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 |
0.326 |
|
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 |
0.334 |
|
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 |
0.347 |
|
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 |
0.405 |
|
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 |
0.72 |
|
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 |
0.355 |
|
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 |
0.306 |
|
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 |
0.407 |
|
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 |
0.407 |
|
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 |
0.507 |
|
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 |
0.33 |
|
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 |
0.369 |
|
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 |
0.342 |
|
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 |
0.412 |
|
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 |
0.344 |
|
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 |
0.368 |
|
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 |
0.349 |
|
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 |
0.38 |
|
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 |
0.35 |
|
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 |
0.351 |
|
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 |
0.636 |
|
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