个人简介

B.S. Nanjing University; Ph.D. Duke University; Postdoctoral research at Howard Hughes Medical Institute, University of California at San Diego

研究领域

Theoretical and Computational Chemistry: combined ab initio quantum mechanical and molecular mechanical methods/computer simulations/with applications to chemical reactions and molecular recognitions in biological systems.

Theoretical and Computational Chemistry: combined ab initio quantum mechanical and molecular mechanical methods, computer simulations, with applications to chemical reactions and molecular recognitions in biological systems. We are interested in the development and application of cutting-edge computational and theoretical methods to understand the inner workings of important biological processes. Due to the complexity of biomolecular systems, the computational methods that we develop and utilize are multiscale in nature, ranging from electronic level description of crucial chemical bonds to coarse-grained approaches for large scale motions and interactions. For the methodology development, we focus on ab initio QM/MM methods, efficient sampling approaches and multiscale simulation methods. For biomolecular simulations, we are currently interested in investigating enzyme mechanism, catalysis and regulation; histone modifications and recognition; and membrane enzymes.

近期论文

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Rooklin, D. W., Modell, A. E., Li, H., Berdan, V., Arora, P. S., and Zhang, Y. Targeting unoccupied surfaces on protein-protein interfaces. J. Am. Chem. Soc. 139, 15560-15563 (2017) Wang, C. and Zhang, Y. Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest. J. Comput. Chem. 38, 169 - 177 (2017) Hou, X., Rooklin, D., Fang, H., and Zhang, Y. Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation. Sci. Rep. 6, 38186 (2016) Zhou, Y., Wang, S., Li, Y., and Zhang, Y. Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of enzyme reactions. Methods Enzymol. 577, 105-118 (2016) Zhou, Y., Xie, D., and Zhang, Y. Amide rotation hindrance predicts proteolytic resistance of cystine-knot peptides. J. Phys. Chem. Lett. 7, 1138-1142 (2016) Rooklin, D., Wang, C., Katigbak, J., Arora, P. S., and Zhang, Y. AlphaSpace: Fragment-centric topographical mapping to target protein–protein interaction interfaces. J. Chem. Inf. Model. 55, 1585–1599 (2015) Lei, J., Zhou, Y., Xie, D., and Zhang, Y. Mechanistic insights into a classic wonder drug-aspirin. J. Am. Chem. Soc. 137, 70-73 (2015)