Publications

Liu, X., Peng, L., and Zhang, J. Z. H. Accurate and efficient calculation of protein-protein binding free energy-interaction entropy with residue type-specific dielectric constants. J. Chem. Inf. Model. 59, 272-281 (2019)

Huang, D., Wen, W., Liu, X., Li, Y., and Zhang, J. Z. H. Computational analysis of hot spots and binding mechanism in the PD-1/PD-L1 interaction. RSC Adv. 9, 14944-14956 (2019)

Xu, M., He, X., Zhu, T., and Zhang, J. Z. H. A fragment quantum mechanical method for metalloproteins. J. Chem. Theory Comput. 15, 1430-1439 (2019)

Yang, Y., He, L., Bao, J., Qi, Y., and Zhang, J. Z. H. Computational analysis for residue-specific CDK2-inhibitor bindings. Chinese Journal of Chemical Physics. 32, 134-142 (2019)

Huang, D., Qi, Y., Song, J., and Zhang, J. Z. H. Calculation of hot spots for protein-protein interaction in p53/PMI-MDM2/MDMX complexes. J. Comput. Chem. 40, 1045-1056 (2019)

Wang, X., Tu, X., Deng, B., Zhang, J. Z. H., and Sun, Z. BAR-based optimum adaptive steered MD for configurational sampling. J. Comput. Chem. 40, 1270-1289 (2019)

Sun, Z., Wang, X., and Zhang, J. Z. H. Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation. Chem. Phys. Lett. 723, 1-10 (2019)

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

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)

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)

Lauvergnat, D., Felker, P., Scribano, Y., Benoit, D. M., and Bačić, Z. H₂, HD, and D₂ in the small cage of structure II clathrate hydrate: Vibrational frequency shifts from fully coupled quantum six-dimensional calculations of the vibration-translation-rotation eigenstates. J. Chem. Phys. 150, 154303 (2019)

Bascom, G. D., Myers, C. G., and Schlick, T. Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub. Proc. Natl. Acad. Sci., 116, 4955-4962 (2019)

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)

Lei, J., Sheng, G., Cheung, P. P. H., Wang, S., Li, Y., Gao, X., Zhang, Y., Wang, Y., and Huang, X. Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc. Natl. Acad. Sci., 116, 845-853 (2019)

Tse, C. K. M., Xu, J., Xu, L., Sheong, F. K., Wang, S., Chow, H. Y., Gao, X., Li, X., Cheung, P. P. H., Wang, D., Zhang, Y., and Huang, X. Intrinsic cleavage of RNA polymerase II adopts a nucleobase-independent mechanism assisted by transcript phosphate. Nature Catalysis, 2, 228-235 (2019)

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 transfer. Chem. 5, 1928-1929 (2019)

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)

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

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)

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)

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 field. J. Chem. Phys. 151, 201101 (2019)

Wang, Y., Verma, P., Jin, X., Truhlar, D. G., and He, X. Revised M06 density functional for main-group and transition-metal chemistry. Proc. Natl. Acad. Sci. U.S.A. 115, 10257–10262 (2018)

Li, Y., Cong, Y., Feng, G., Zhong, S., Zhang, J. Z. H., Sun, H., and Duan, L. The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction. Struct. Dyn. 5, 064101 (2018)

Li, P., Liu, F., Jia, X., Shao, Y., Hu, W., Zheng, J., and Mei, Y. Efficient computation of free energy surfaces of Diels–Alder reactions in explicit solvent at ab initio QM/MM level. Molecules. 23, 2487 (2018)

Li, P., Jia, X., Pan, X., Shao, Y., and Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semi-empirical reference potential. I. weighted thermodynamics perturbation. J. Chem. Theory Comput. 14, 5583-5596 (2018)

Wang, M., Mei, Y., and Ryde, U. Predicting relative binding affinity using nonequilibrium QM/MM simulations. J. Chem. Theory Comput. 14, 6613-6622 (2018)

Bačić, Z., Vlček, V., Neuhauser, D., and Felker, P. M. Effects of symmetry breaking on the translation–rotation eigenstates of H₂, HF, and H₂O inside the fullerene C₆₀. Faraday Discuss. 212, 547-567 (2018)

Yao, Z., Jiang, S., Zhang, L., Gao, B., He, X., Zhang, J. Z. H., and Wei, D. Crius: A novel fragment‐based algorithm of de novo substrate prediction for enzymes. Protein Sci. 27, 1526-1534 (2018)

Zhu, T., Wu, C., Song, J., Reimers, J. R., and Li, Y. Polarization effect within a protein crystal: A molecular dynamics simulation study. Chem. Phys. Lett. 706, 303-307 (2018)

Qiu, L., Shen, C., Song, J., Zhang, Y., and Zhang, J. Z. H. Functional loop dynamics of the S-component of ECF transporter FolT. Mol. Phys. 116, 2613-2621 (2018)

Cai, Y., Fu, I., Geacintov, N. E., Zhang, Y., and Broyde, S. Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognition. DNA Repair. 65, 73-78 (2018)

Wang, Y., Liu, J., Li, J., and He, X. Fragment-based quantum mechanical calculation of protein–protein binding affinities. J. Comput. Chem. 39, 1617-1628 (2018)

Bačić, Z. Perspective: Accurate treatment of the quantum dynamics of light molecules inside fullerene cages: Translation-rotation states, spectroscopy, and symmetry breaking. J. Chem. Phys. 149, 100901 (2018)

Chen, J., Duan, L., Ji, C., and Zhang, J. Z. H. Computational study of PCSK9-EGFA complex with effective polarizable bond force field. Front. Mol. Biosci. 4, 101 (2018)

Zhou, Y., Liu, X., Zhang, Y., Peng, L. and Zhang, J. Z. H. Residue-specific free energy analysis in ligand bindings to JAK2. Mol. Phys. 116, 2633-2641 (2018)

Li, Y., Wang, X., Ren, L., Cao, X., Ji, C., Xia, F., and Zhang, J. Z. H. Electrostatic polarization effect on cooperative aggregation of full length human islet amyloid. J. Chem. Inf. Model.  58, 1587-1595 (2018)

Sun, H., Duan, L., Chen, F., Liu, H., Wang, Z., Pan, P., Zhu, F., Zhang, J. Z. H., and Hou, T. Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches. Phys. Chem. Chem. Phys. 20, 14450-14460 (2018)

Jain, S., Bayrak, C. S., Petingi, L., and Schlick, T. Dual graph partitioning highlights a small group of pseudoknot-containing RNA submotifs. Genes. 9, 371 (2018)

Schlick, T. Adventures with RNA graphs. Methods. 143, 16-33, 2018

Bascom, G. D. and Schlick, T. Chromatin fiber folding directed by cooperative histone tail acetylation and linker histone binding. Biophys. J. 114, 2376-2385 (2018)

Cuendet, M. A., Margul, D. T., Schneider, E., Vogt-Maranto, L., and Tuckerman, M. E. Endpoint-restricted adiabatic free energy dynamics approach for the exploration of biomolecular conformational equilibria. J. Chem. Phys. 149, 072316 (2018)

Silletta, E. V., Tuckerman, M. E., and Jerschow, A. Unusual protont transfer kinetics in water at the temperature of maximum density. Phys. Rev. Lett. 121, 076001 (2018)

Sun, X., Zhang, P., Lai, Y., Williams, K. L., Cheung, M. S., Dunietz, B. D., and Geva, E. Computational study of charge-transfer dynamics in the carotenoid–porphyrin–C60 molecular triad solvated in explicit tetrahydrofuran and its spectroscopic signature. J. Phys. Chem. C. 122, 11288-11299 (2018)

Cong, Y., Li, Y., Jin, K., Zhong, S., Zhang, J. Z. H., Li, H., and Duan, L. Exploring the reasons for decrease in binding affinity of HIV-2 against HIV-1 protease complex using interaction entropy under polarized force field. Front. Chem. 6, 380 (2018)

Liu, J., Zhang, J. Z. H., and He, X. Probing the ion-specific effects at the water/air interface and water-mediated ion pairing in sodium halide solution with ab initio molecular dynamics. J. Phys. Chem. B. 122, 10202-10209 (2018)

Jain, S., Laederach, A., Ramos, S. B. V., and Schlick, T. A pipeline for computational design of novel RNA-like topologies. Nucleic Acids Res. 46, 7040–7051 (2018)

Shiga, M. and Tuckerman, M. E. Finding free-energy landmarks of chemical reactions. J. Phys. Chem. Lett. 9, 6207−6214 (2018)

Chen, J., Huang, M., and Xia, F. Conformer-related pathways in cycloaddition of vinylaziridines and alkynes catalyzed by rhodium(I)-complex. Chem. Phys. Lett. 713, 21-25 (2018)

Mu, H., Zhang, Y., Geacintov, N. E., and Broyde, S. Lesion sensing during initial binding by yeast XPC/Rad4: Toward predicting resistance to nucleotide excision repair. Chem. Res. Toxicol. 31, 1260-1268 (2018)

Hou, X., Rooklin, D., Yang, D., Liang, X., Li, K., Lu, J., Wang, C., Xiao, P., Zhang, Y., Sun, J., and Fang, H. Computational strategy for bound state structure prediction in structure-based virtual screening: A case study of protein tyrosine phosphatase receptor type O inhibitors. J. Chem. Inf. Model. 58, 2331-2342 (2018)