Publications

51.

Tang, X., Wang, J., Zhang, J., Miao, Y., Zhao, Y., Gao, B., and Zhang, L. Rational design of lipase MAS1 for the long-chain substrate affinityJournal of East China University of Science and Technology, 49, 529-535 (2023)

52.

Li, Y., Wang, Y., Zhang, R. M., He, X., and Xu, X. Comprehensive theoretical study on four typical intramolecular hydrogen shift reactions of peroxy radicals: Multireference character, recommended model chemistry, and kineticsJ. Chem. Theory Comput. 19, 3284–3302 (2023)

53.

Zha, J. and Xia, F. Developing hybrid all-atom and ultra-coarse-grained models to investigate taxol-binding and dynein interactions on microtubulesJ. Chem. Theory Comput. 19, 5621–5632 (2023)

54.

Li, Z., Portillo-Ledesma, S., and Schlick, T. Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture dataCurr. Opin. Cell Biol. 83, 102209 (2023)

55.

Guo, J., Xue, Y., Zhao, C., Zhao, J., Gao, Z., Mei, Y., and Song, Y.-Y. Integrated separation-electrochemical detection device based on wood column for online identification of enantiomerNano Res. (2023)

56.

Li, Y., Yang, J., and He, X. Characterizing polyproline II conformational change of collagen superhelix unit on adsorption on gold surfaceNanoscale Adv. 5, 5322-5331 (2023)

57.

Jiang, Y., Wan, Z., He, X., and Yang, J. Fine-tuning electrolyte concentration and metal–organic framework surface toward actuating fast Zn2+ dehydration for aqueous Zn-ion batteriesAngew. Chem. 62, e202307274 (2023)

58.

Zhang, J., Kriebel, C. N., Wan, Z., Shi, M., Glaubitz, C., and He, X. Automated fragmentation quantum mechanical calculation of 15N and 13C chemical shifts in a membrane proteinJ. Chem. Theory Comput. 19, 7405–7422 (2023)

59.

Yu, L., He, X., Fang, X., Liu, L., and Liu, J. Deep learning with geometry-enhanced molecular representation for augmentation of large-scale docking-based virtual screeningJ. Chem. Inf. Model. 63, 6501–6514 (2023)

60.

Vindel-Zandbergen, P., Kȩdziera, D., Żółtowski, M., Kłos, J., Żuchowski, P., Felker, P. M., Lique, F., and Bačić, Z. H2O–HCN complex: A new potential energy surface and intermolecular rovibrational states from rigorous quantum calculationsJ. Chem. Phys. 159, 174302 (2023)

61.

Liu, Z., Hu, H., and Sun, X. Multistate reaction coordinate model for charge and energy transfer dynamics in the condensed phaseJ. Chem. Theory Comput. 19, 7151–7170 (2023)

62.

Yang, Y., Lyu, X., Cong, Y., Miao, T., Fang, B., Zhang, C., Shen, Q., Matthews, M., Fisher, A. J., Zhang, J. Z. H.Zhang, L., and Yang, R. A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reactionInt. J. Biol. Macromol. 253, 127093 (2023)

63.

Duan, L., Tang, B., Luo, S., Xiong, D., Wang, Q., Xu, X., and Zhang, J. Z. H. Entropy driven cooperativity effect in multi-site drug optimization targeting SARS-CoV-2 papain-like proteaseCell. Mol. Life Sci. 80, 313 (2023)

64.

Liu, X., Zheng, L., Qin, C., Li, Y., Zhang, J. Z. H., and Sun, Z. Screening power of end-point free-energy calculations in cucurbituril host–guest systemsJ. Chem. Inf. Model. 63, 6938–6946 (2023)

65.

Zhao, C., Yang, G., Zhang, S., He, X., Zhong, Y., and Gao, X. Enhanced breathing effect of nanoporous UIO-66-DABA metal–organic frameworks with coordination defects for high selectivity and rapid adsorption of Hg(II)ACS Appl. Nano Mater. 6, 18372–18380 (2023)

66.

Pan, X., Snyder, R., Wang, J.-N., Lander, C., Wickizer, C., Van, R., Chesney, A., Xue, Y., Mao, Y., Mei, Y., Pu, J., and Shao, Y. Training machine learning potentials for reactive systems: A Colab tutorial on basic models.  J. Comput. Chem. (2023)

67.

Li, Z. and Schlick, T. Hi-BDiSCO: Folding 3D mesoscale genome structures from Hi-C data using brownian dynamicsNucleic Acids Res. gkad1121 (2023)

68.

Zhang, C., Miao, Y., Feng, Y., Wang, J., Tian, Z., Dong, J., ... and Zhang, L. Umami polypeptide detection system targeting the human T1R1 receptor and its taste-presenting mechanismBiomaterials 287, 121660 (2022)

69.

Chen, S., Ding, X., Sun, C. Wang, F., He, X., Watts, A., and Zhao X. Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and UptakeInt. J. Mol. Sci. 23, 6913 (2022)

70.

Zhang, H., Saravanan, K. M., Yang, Y., Wei, Y., Yi, P., and Zhang, J. Z. H. Generating and screening de novo compounds against given targets using ultrafast deep learning models as core componentsBrief. Bioinform. 23, bbac226 (2022)

71.

Xiong, D., Zhao, X., Luo, S., Cong, Y., Zhang, J. Z. H., and Duan, L. Immune escape mechanisms of SARS-CoV-2 delta and omicron variants against two monoclonal antibodies that received emergency use authorizationJ. Phys. Chem. Lett. 13, 6064–6073 (2022)

72.

Wang, H., Pan, X., Zhang, Y., Wang, X., Xiao, X., and Ji, C. MolHyb: A web server for structure-based drug design by molecular hybridizationJ. Chem. Inf. Model. 62, 2916–2922 (2022)

73.

Liu, J., Lan, J., and He, X. Toward high-level machine learning potential for water based on quantum fragmentation and neural networksJ. Phys. Chem. A (2022)

74.

Karashima, S., Humeniuk, A., Glover, W. J., and Suzuki, T. Ultrafast photoisomerization of ethylene studied using time-resolved extreme ultraviolet photoelectron spectroscopy. J. Phys. Chem. A (2022)

75.

Zhang, D., Xia, S., and Zhang, Y. Accurate prediction of aqueous free solvation energies using 3D atomic feature-based graph neural network with transfer learningJ. Chem. Inf. Model. 62, 1840–1848 (2022)

76.

Yang, C. and Zhang, Y. Delta machine learning to improve scoring-ranking-screening performances of protein–ligand scoring functions. J. Chem. Inf. Model  62, 2696–2712 (2022)

77.

Cong, Y., Li, M., Qi, Y., and Zhang, J. Z. H. A fast–slow method to treat solute dynamics in explicit solventPhys. Chem. Chem. Phys. 24, 14498-14510 (2022)

78.

Xiong, Y., Zeng, J., Xia, F., Cui, Q., Deng, X., and Xu, X. Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange processJ. Comput. Chem. 43, 906-916 (2022)

79.

Zelovich, T., Simari, C., Nicotera, I., Dekel, D. R., and Tuckerman, M. E. The impact of carbonation on hydroxide diffusion in nano-confined anion exchange membranesJ. Mater. Chem. A. 10, 11137-11149 (2022)

80.

Xu, J., Xue, Y., Jian, X., Zhao, Y., Dai, Z., Xu, J., … Mei, Y., and Song, Y. Y. Understanding of chiral site-dependent enantioselective identification on plasmon-free semiconductor based SERS substrateChem. Sci. (2022)

81.

Yang, L., Feng, J., Wang, J. N., Gao, Z., Xu, J., Mei, Y., and Song, Y. Y. Engineering large-scaled electrochromic semiconductor films as reproductive SERS substrates for operando investigation at the solid/liquid interfacesChin. Chem. Lett. (2022)

82.

Cao, L., Zeng, J., Wang, B., Zhu, T., and Zhang, J. Z. H. Ab initio neural network MD simulation of thermal decomposition of a high energy material CL-20/TNTPhys. Chem. Chem. Phys. 24, 11801-11811 (2022)

83.

Pan, X., Wang, H., Zhang, Y., Wang. X., Li, C., Ji, C., and Zhang, J. Z. H. AA-score: A new scoring function based on amino acid-specific interaction for molecular dockingJ. Chem. Inf. Model. 62, 2499–2509 (2022)

84.

Zhang, X., Mao, J., Wei, M., Qi, Y., and Zhang, J. Z. H. HergSPred: Accurate classification of hERG blockers/nonblockers with machine-learning modelsJ. Chem. Inf. Model. 62, 1830–1839 (2022)

85.

Lu, J. and Zhang, Y. Unified deep learning model for multitask reaction predictions with explanationJ. Chem. Inf. Model. 62, 1376–1387 (2022)

86.

Zheng, L., Yang, Y., Bao, J., He, L., Qi, Y., and Zhang, J. Z. H. Discovery of novel inhibitors of CDK2 using docking and physics- based binding free energy calculationChem. Biol. Drug Des. 1– 12 (2022)

87.

Liang, J., Chen, Y., Bu, S., Song, S., Yang, J., Wang, M., and Yuan, Q. Computational study of the C2P4 monolayer as a stable two-dimensional material with high carrier mobility: Implications for nanoelectronic devicesACS Appl. Nano Mater. 5, 6972–6979 (2022)

88.

Miao, Y., Ni, H., Zhang, X., Zhi, F., Long, X., Yang, X., He, X., and Zhang, L. Investigating mechanism of sweetness intensity differences through dynamic analysis of sweetener–T1R2–membrane systemsFood Chem. 374, 131807 (2022)

89.

Tuckerman, M. E. The curse of dimensionality loses its powerNat. Comput. Sci. 2, 6–7 (2022)

90.

Qu, K., Xu, J., Xue, Y., Guo, J., Gao, Z., Song, Y.-Y., and Mei, Y. Near infrared light-driven photothermal effect on homochiral Au/TiO2 nanotube arrays for enantioselective desorptionAnal. Chem. 94, 588–592 (2022)

91.

 Kleimeier, N. F., Liu, Y., Turner, A. M., Young, L. A., Chin, C.-H., Yang, T., He, X., Lo, J., Cheng, B. M., and Kaiser, R. I. Excited state photochemically driven surface formation of benzene from acetylene ices on Pluto and in the outer solar systemPhys. Chem. Chem. Phys. 24, 1424-1436 (2022)

92.

Tinnin, J., Bhandari, S., Zhang, P., Geva, E., Dunietz, B. D., Sun, X., and Cheung, M. S. Correlating interfacial charge transfer rates with interfacial molecular structure in the tetraphenyldibenzoperiflanthene/C70 organic photovoltaic systemJ. Phys. Chem. Lett. 13, 763–769 (2022)

93.

Wei, M., Zhang, X., Pan, X., Wang, B., Ji, C., Qi, Y., and Zhang, J. Z. H. HobPre: accurate prediction of human oral bioavailability for small moleculesJ. Cheminform. 14, 1 (2022)

94.

Qiu L., Song J., Zhang J.Z.H. (2022) Computational Alanine Scanning Reveals Common Features of TCR/pMHC Recognition in HLA-DQ8-Associated Celiac Disease. In: Vanhaelen Q. (eds) Computational Methods for Estimating the Kinetic Parameters of Biological Systems. Methods in Molecular Biology, vol 2385. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1767-0_13

95.

Jin, S., Wang, J.-N., Xue, Y., Li, P., and Mei, Y. Selectivity of parvalbumin B protein binding to Ca2+ and Mg2+ at an ab initio QM/MM level using the reference-potential methodChin. J. Chem. Phys. 34, 741 (2022)

96.

Xu, M., Felker, P. M., and Bačić, Z. H2O inside the fullerene C60: Inelastic neutron scattering spectrum from rigorous quantum calculationsJ. Chem. Phys. 156, 124101 (2022)

97.

Zelovich, T. and Tuckerman, M. E. Controlling hydronium diffusivity in model proton exchange membranesJ. Phys. Chem. Lett. 13, 2245–2253 (2022)

98.

Metz, M. P., Shahbaz, M., Song, H., Vogt-Maranto, L., Tuckerman, M. E., and Szalewicz, K. Crystal structure predictions for 4-amino-2,3,6-trinitrophenol using a tailor-made first-principles-based force fieldCryst. Growth Des. 22, 1182–1195 (2022)

99.

Spittle, S., Poe, D., Doherty, B., Kolodziej, C., Heroux, L., Haque, M. A., … Tuckerman, M., … and Sangoro, J. Evolution of microscopic heterogeneity and dynamics in choline chloride-based deep eutectic solventsNat. Commun. 13, 219 (2022)

100.

Li, Z. and Zhang, J. Z. H. Mutational effect of some major COVID-19 variants on binding of the S protein to ACE2Biomolecules. 12, 572 (2022)

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