Publications

301.

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

302.

Tian, S., Zeng, J., Liu, X., Chen, J., Zhang, J. Z. H., and Zhu, T. Understanding the selectivity of inhibitors toward PI4KIIIα and PI4KIIIβ based molecular modeling. Phys. Chem. Chem. Phys. 21, 22103-22112 (2019)

303.

Luo, H., Liu, J., He, X., and Li, J. Low-temperature polymorphic transformation of β-lactam antibiotics. Crystals. 9, 460 (2019)

304.

Yang, H., Zhang, F., Huang, C.-J., Liao, J., Han, Y., Hao, P., Chu, Y., Lu, X., Li, W., Yu, H., and Kang, J. Mps1 regulates spindle morphology through MCRS1 to promote chromosome alignment. Mol. Biol. Cell. 30, 1051-1128 (2019)

305.

Jain, S., Tao, Y., and Schlick, T. Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologiesJ. Struct. Biol. 209, 107438 (2020)

306.

Petkov, B. K., Gellen, T. A., Farfan, C. A., Carbery, W. P., Hetzler, B. E., Trauner, D., Li, X., Glover, W. J., Ulness, D. J., and Turner, D. B. Two-dimensional electronic spectroscopy reveals the spectral dynamics of Förster resonance energy transferChem. 5, 1928-1929 (2019)

307.

Wang, Y., Verma, P., Zhang, L., Li, Y., Liu, Z., Truhlar, D. G., and He, X. M06-SX screened-exchange density functional for chemistry and solid-state physics. Proc. Natl. Acad. Sci. U.S.A. 117, 2294-2301 (2020)

308.

Xu, J., Liu, J., Liu, J., Hu, W., He, X., and Li, J. Phase transition of ice at high pressures and low temperatures. Molecules. 25, 486 (2020)

309.

Rogal, J., Schneider, E., and Tuckerman, M. E. Neural-network-based path collective variables for enhanced sampling of phase transformationsPhys. Rev. Lett. 123, 245701 (2019)

310.

Liu J., He X. (2020) QM Implementation in Drug Design: Does It Really Help? In: Heifetz A. (eds) Quantum Mechanics in Drug Discovery. Methods in Molecular Biology, vol 2114. Humana, New York, NY

311.

Meng, G., Tariq, M., Jain, S., Elmetwaly, S., and Schlick, T. RAG-Web: RNA structure prediction/design using RNA-As-Graphs. Bioinformatics. 36, 647–648 (2020)

312.

Mao, J., Aladin, V., Jin, X., Leeder, A. J., Brown, L. J., Brown, R. C. D., He, X., Corzilius, B., and Glaubitz, C. Exploring protein structures by DNP-enhanced methyl solid-state NMR spectroscopy. J. Am. Chem. Soc. 141, 19888-19901 (2019)

313.

Gao, Z., Bao, J., Shi, S., Zhang, X., Gao, Y., and Zhu, T. Effect of mutations on drug resistance of smoothened receptor toward inhibitors probed by molecular modelingChem. Phys. Lett. 741, 137126 (2020)

314.

Wu, Z., Zhang, Y., Zhang, J. Z., Xia, K., and Xia, F. Determining optimal coarse-grained representation for biomolecules using internal cluster validation indexesJ. Comput. Chem. 41, 14-20 (2019)

315.

Sun, Z., Wang, X., and Zhang, J. Z. H. Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR–ligand binding. Phys. Chem. Chem. Phys. 22, 1511-1524 (2020)

316.

Zeng, J., Cao, L., Chin, C.-H., Ren, H., Zhang, J. Z. H., and Zhu, T. ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations. Phys. Chem. Chem. Phys. 22, 683-691 (2020)

317.

Shao, Y., Mei, Y., Sundholm, D., and Kaila, V. R. I. Benchmarking the performance of time-dependent density functional theory methods on biochromophoresJ. Chem. Theory Comput. 16, 587-600 (2019)

318.

Glover, W. J. and Schwartz, B. J. The fluxional nature of the hydrated electron: Energy and entropy contributions to aqueous electron free energies. J. Chem. Theory Comput. 16, 1263-1270 (2020)

319.

Marsiglia, W., Katigbak, J., Zheng, S., Mohammadi, M., Zhang, Y., and Traaseth N. A conserved allosteric pathway in tyrosine kinase regulation. Structure. 27, 1308-1315.e3 (2019)

320.

Yang, Y., Lu, J., Yang, C., and Zhang, Y. Exploring fragment-based target specific ranking protocol with machine learning on cathepsin S. J. Comput. Aided Mol. Des. 33, 1095-1105 (2019)

321.

Lu, J., Hou, X., Wang, C., and Zhang Y. Incorporating explicit water molecules and ligand conformation stability in machine-learning scoring functions. J. Chem. Inf. Model. 59, 4540-4549 (2019)

322.

Glover, W. J., Paz, A. S. P., Thongyod, W., and Punwong, C. Analytical gradients and derivative couplings for dynamically weighted complete active space self-consistent fieldJ. Chem. Phys. 151, 201101 (2019)

323.

Wang, T., Su, X., Zhang, X., Nie, X., Huang, L., Zhang, X., Sun, X., Luo, Y., and Zhang, G. Aggregation-induced dual-phosphorescence from organic molecules for non-doped light-emitting diodesAdv. Mater. 31, 1904273 (2019)

324.

Sun, X. Hybrid equilibrium-nonequilibrium molecular dynamics approach for two-dimensional solute-pump/solvent-probe spectroscopyJ. Chem. Phys. 151, 194507 (2019)

325.

Wang, M., Mei, Y., and Ryde, U. Host-guest relative binding affinities at density-functional theory level from semiempirical molecular dynamics simulations. J. Chem. Theory Comput. 15, 2659-2671 (2019)

326.

Zhang, Y., Xia, K., Cao, Z., Gräter, F., and Xia, F. A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data. Phys. Chem. Chem. Phys. 21, 9720-9727 (2019)

327.

Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., and Hou, T. End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chem. Rev. 119, 9478-9508 (2019)

328.

Han, Y., Liu, J., Huang, L., He, X., and Li, J. Predicting the phase diagram of solid carbon dioxide at high pressure from first principles. npj Quantum Materials. 4, 10 (2019)

329.

Zhang, L., Mei, D., Wu, Y., Shen, C., Hu, W., Zhang, L., Li, J., Wu, Y., and He, X. Syntheses, structures, optical properties, and electronic structures of Ba6Cu2GSn4S16 (G= Fe, Ni) and Sr6D2FeSn4S16 (D= Cu, Ag). J. Solid State Chem. 272, 69-77 (2019)

330.

Duan, L., Guo, X., Cong, Y., Feng, G., Li, Y., and Zhang, J. Z. H. Accelerated molecular dynamics simulation for helical proteins folding in explicit water. Front Chem. 7, 540 (2019)

331.

Verma, P., Janesko, B. G., Wang, Y., He, X., Scalmani, G., Frisch, M. J., and Truhlar, D. G. M11plus: A range-separated hybrid meta functional with both local and rung-3.5 correlation terms and high across-the-board accuracy for chemical applications. J. Chem. Theory Comput. 15, 4804-4815 (2019)

332.

He, L., Bao, J., Yang, Y., Dong, S., Zhang, L., Qi, Y., and Zhang, J. Z. H. Study of SHMT2 inhibitors and their binding mechanism by computational alanine scanning. J. Chem. Inf. Model. 59, 3871-3878 (2019)

333.

Xu, M., Zhu, T., and Zhang, J. Z. H. Molecular dynamics simulation of zinc ion in water with an ab initio based neural network potential. J. Phys. Chem. A. 123, 6587-6595 (2019)

334.

Liu, J., Sun, H., Glover, W. J., and He, X. Prediction of excited-state properties of oligoacene crystals using fragment-based quantum mechanical method. J. Phys. Chem. A. 123, 5407-5417 (2019)

335.

Lu, J., Wang, C., and Zhang, Y. Predicting molecular energy using force-field optimized geometries and atomic vector representations learned from an improved deep tensor neural network. J. Chem. Theory Comput. 15, 4113-4121 (2019)

336.

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

337.

Lu, Q., He, X., Hu, W., Chen, X., and Liu, J. Stability, vibrations, and diffusion of hydrogen gas in clathrate hydrates: Insights from ab initio calculations on condensed-phase crystalline structures. J. Phys. Chem. C. 123, 12052-12061 (2019)

338.

Li, K., Hou, X., Li, R., Bi, W., Yang, F., Chen, X., Xiao, P., Liu, T., Lu, T., Zhou, Y., Tian, Z., Shen, Y., Zhang, Y., Wang, J., Fang, H., Sun, J., and Yu, X. Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22. J. Biol. Chem. 294, 8653-8663 (2019)

339.

Cao, H., Wang, J., He, L., Qi, Y., and Zhang, J. Z. H. DeepDDG: Predicting the stability change of protein point mutations using neural networks. J. Chem. Inf. Model. 59, 1508-1514 (2019)

340.

Verma, P., Wang, Y., Ghosh, S., He, X., and Truhlar, D. G. Revised M11 exchange-correlation functional for electronic excitation energies and ground-state properties. J. Phys. Chem. A. 123, 2966-2990 (2019)

341.

Luo, H., Hao, X., Gong, Y., Zhou, J., He, X., and Li, J. Rational crystal polymorph design of olanzapine. Cryst. Growth Des. 19, 2388-2395 (2019)

342.

Sun, Z., Wang, X., Zhang, J. Z. H., and He, Q. Sulfur-substitution-induced base flipping in the DNA duplex. Phys. Chem. Chem. Phys. 21, 14923-14940 (2019)

343.

Tuckerman, M. E. Machine learning transforms how microstates are sampled. Science. 365, 982-983 (2019)

344.

Xiao, Z., Cong, Y., Huang, K., Zhong, S., Zhang, J. Z. H., and Duan, L. Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy. Phys. Chem. Chem. Phys. 21, 20951-20964 (2019)

345.

Zelovich, T., Vogt-Maranto, L., Hickner, M. A., Paddison, S. J., Bae, C., Dekel, D. R., and Tuckerman, M. E. Hydroxide ion diffusion in anion-exchange membranes at low hydration: Insights from ab initio molecular dynamics. Chem. Mater. 31, 5778-5787 (2019)

346.

Chen, J., Yin, B., Pang, L., Wang, W., Zhang, J. Z. H., and Zhu, T. Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologiesJ. Biomol. Struct. Dyn. 1-15 (2019)

347.

Shtukenberg, A. G., Tan, M., Vogt-Maranto, L., Chan, E. J., Xu, W., Yang, J., Tuckerman, M. E., Hu, C. T., and Kahr, B. Melt crystallization for paracetamol polymorphism. Cryst. Growth Des. 19, 4070-4080 (2019)

348.

Li, P., Liu, F., Shao, Y., and Mei, Y. Computational insights into endo/exo selectivity of the Diels-Alder reaction in explicit solvent at ab initio quantum mechanical/molecular mechanical level. J. Phys. Chem. B. 123, 5131-5138 (2019)

349.

Zhang, Z., Liu, X., Yan, K., Tuckerman, M. E., and Liu, J. Unified efficient thermostat scheme for the canonical ensemble with holonomic or isokinetic constraints via molecular dynamics. J. Phys. Chem. A. 123, 6056-6079 (2019)

350.

Liu, X., Zhao, Y., and Zhang, J. Z. H. Molecular mechanism of ligand bindings to Zika virus at SAM site. Chem. Phys. Lett. 735, 136771 (2019)

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