个人简历

Yingkai Zhang received his B.S. degree in Chemistry from Nanjing University in 1993 and his Ph.D. degree in Chemistry from Duke University in 2000. His postdoctoral research was conducted at Howard Hughes Medical Institute, University of California at San Diego from 2000 to 2003. He was a recipient of the National Science Foundation CAREER Award (2005), the NYSTAR James D. Watson Young Investigator Award (2005), and Whitehead Fellowship for Junior Faculty in Biomedical and Biological Sciences (2006).

研究领域

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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."Professor Zhang and his research group are interested in developing and applying novel computational methods to elucidate novel physical-chemical insights into important biological processes, and to rational design their modulators for probing important cellular pathways and for therapeutic use. Their current research projects include integrated molecular modeling and machine learning, rational modulator design to target protein-protein interactions, and computer simulations of biomolecular 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.
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近期论文

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)