Publications

301.

Wang, Z., Han, Y., Li, J., He, X. Combining the fragmentation approach and neural network potential energy surfaces of fragments for accurate calculation of protein energy. J. Phys. Chem. B. 124, 3027-3035 (2020)

302.

Felker, P. M. and Bačić, Z. Benzene–H2O and benzene–HDO: Fully coupled nine-dimensional quantum calculations of flexible H2O/HDO intramolecular vibrational excitations and intermolecular states of the dimers, and their infrared and Raman spectra using compact basesJ. Chem. Phys. 152, 124103 (2020)

303.

Duan, G., Ji, C., and Zhang, J. Z. H. Developing an effective polarizable bond method for small molecules with application to optimized molecular dockingRSC Adv. 10, 15530-15540 (2020)

304.

Cong, Y., Huang, K., Li, Y., Zhong, S., Zhang, J. Z. H., and Duan, L. Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin–biotin binding. Nanoscale. 12, 7134-7145 (2020)

305.

Huang, L., Han, Y., He, X., and Li, J. Ab initio-enabled phase transition prediction of solid carbon dioxide at ultra-high temperatures. RSC Adv. 10, 236-243 (2020)

306.

Qi, Y. and Zhang, J. Z. H. DenseCPD: Improving the accuracy of neural-network-based computational protein sequence design with DenseNetJ. Chem. Inf. Model. 60, 1245-1252 (2020)

307.

Tinnin, J., Bhandari, S., Zhang, P., Aksu, H., Maiti, B., Geva, E., Dunietz, B. D., Sun, X., and Cheung, M. S. Molecular-level exploration of the structure-function relations underlying interfacial charge transfer in the subphthalocyanine/C60 organic photovoltaic systemPhys. Rev. Appl. 13, 054075 (2020)

308.

Wang, B., Qi, Y., Gao, Y., and Zhang, J. Z. H. A method for efficient calculation of thermal stability of proteins upon point mutationsPhys. Chem. Chem. Phys. 22, 8461-8466 (2020)

309.

Liu, L., Gao, H., Yang, S.-Q., Chen, X.-C., Lu, Y., Liu, Y., and Xia, F. Ir-catalyzed tandem hydroformylation-transfer hydrogenation of olefins with (trans-/cis-)formic acid as hydrogen source in presence of 1,10-phenanthroline. J. Catal. 385, 183-193 (2020)

310.

Li, F., Zhang, J. Z., and Xia, F. How CuCl and CuCl2 insert into C–N bonds of diazo compounds: An electronic structure and mechanistic study. J. Phys. Chem. A. 124, 2029-2035 (2020)

311.

Huang, L., Han, Y., Liu, J., He, X., and Li, J. Ab initio prediction of the phase transition for solid ammonia at high pressuresSci. Rep. 10, 7546 (2020)

312.

Wang, R., Cong, Y., Li, M., Bao, J., Qi, Y., and Zhang, J. Z. H. Molecular mechanism of selective binding of NMS-P118 to PARP-1 and PARP-2: A computational perspective. Front. Mol. Biosci. 7, 50 (2020)

313.

Xu, R., Hu, Z., Wang, X., Liu, Y., Zhou, Z., Xu, J., Sun, Z., Sun, H., and Chen, J. Intramolecular charge transfer in 5-halogen cytidines revealed by femtosecond time-resolved spectroscopyJ. Phys. Chem. B. 124, 2560-2567 (2020)

314.

Liu, J. and He, X. Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquidsPhys. Chem. Chem. Phys. 22, 12341-12367 (2020)

315.

Li, M., Teng, B., and Zhang, J. Z. H. Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy. J. Mol. Model. 26, 31 (2020)

316.

Jain, S., Zhu, Q., Paz, A. S. P., and Schlick, T. Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library. BBA General Subjects. 1864, 129534 (2020)

317.

Zhang, W., Liu, J., Jin, X., Gu, X., Zeng, X. C., He, X., and Li, H. Quantitative prediction of aggregation‐induced emission: A full quantum mechanical approach to the optical spectraAngew. Chem. Int. Ed. 59, 2-8 (2020)

318.

Huang, D., Tian, S., Qi, Y., and Zhang, J. Z. H. Binding modes of small-molecule inhibitors to the EED pocket of PRC2. ChemPhysChem. 21, 263-271 (2020)

319.

Myers, C. G., Olins, D. E., Olins, A. L., and Schlick, T. Mesoscale modeling of nucleosome-binding antibody PL2-6: Mono- versus bivalent chromatin complexes. Biophys. J. 118, 2066-2076 (2020)

320.

Li, X., Cong, Y., Ma, M., You, Z.-N., Gao, B., Zhang, J. Z. H., and Zhang, L. An energy optimization strategy based on the perfect conformation of prolyl endopeptidase for improving catalytic efficiency. J. Agric. Food Chem. 68, 5129–5137 (2020)

321.

Li, Z., Bao, J., Qi, Y., and Zhang, J. Z. H. Computational approaches to studying methylated H4K20 recognition by DNA repair factor 53BP1. Phys. Chem. Chem. Phys. 22, 6136-6144 (2020)

322.

Sridhara, A., Farra, S. E., Portellab, G., Schlick, T., Orozco, M., and Collepardo-Guevara, R. Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry. Proc. Natl. Acad. Sci. U.S.A. 117, 7216–7224 (2020)

323.

Tong, Z., Huai, Z., Mei, Y., and Mo, Y. Reproducing the low-temperature excitation energy transfer dynamics of phycoerythrin 545 light-harvesting complex with a structure-based model Hamiltonian. J. Chem. Phys. 152, 135101 (2020)

324.

Tian, S., Ji, C., and Zhang, J. Z. H. Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarizationJ. Biomol. Struct. Dyn. 39, 1588-1599 (2021)

325.

Sadek, J., Wuo, M. G., Rooklin, D., Hauenstein, A., Hong, S. H., Gautam, A., Wu, H., Zhang, Y., Cesarman, E., and Arora, P. S. Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics. Nat. Commun. 11, 1786 (2020)

326.

Guo, J., Yang, L., Gao, Z., Zhao, C., Mei, Y., and Song, Y.-Y. Insight of MOF environment-dependent enzyme activity via MOFs-in-nanochannels configurationACS Catal. 10, 5949–5958 (2020)

327.

Cong, Y., Duan, L., Huang, K., Bao, J., and Zhang, J. Z. H. Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor. J. Biomol. Struct. Dyn. 39, 1588-1599 (2020)

328.

Katigbak, J., Li, H., Rooklin, D., and Zhang, Y. AlphaSpace 2.0: Representing concave biomolecular surfaces using β-clusters. J. Chem. Inf. Model. 60, 1494-1508 (2020)

329.

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)

330.

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)

331.

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

332.

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)

333.

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)

334.

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)

335.

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)

336.

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)

337.

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)

338.

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

339.

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)

340.

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)

341.

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)

342.

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)

343.

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)

344.

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)

345.

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)

346.

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)

347.

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)

348.

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)

349.

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)

350.

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)

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