Yingkai Zhang

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

Phone: 212-998-7882
Office: Waverly Building, 24 Waverly Place, Room 1166D
Lab Homepage

Areas of Research/Interest
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.

Research Description
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.

J. Lei, Y. Zhou, D. Xie and Y. Zhang, J. Am. Chem. Soc. , 137, 70-73 (2015).

Mechanistic Insights into a Classic Wonder Drug - Aspirin

J. Zhou, M. Li, N. Chen, S. Wang, H. B. Luo, Y. Zhang, and R. Wu, ACS Chem. Biol. , 10 , 687-692 (2015).

Computational Design of a Time-Dependent Histone Deacetylase 2 Selective Inhibitor

X. Xiao, N. Kallenbach and Y. Zhang, J. Chem. Theory Comput., 10, 4152-4159 (2014).

Peptide Conformation Analysis using an Integrated Bayesian Approach

N. Zhou, Z. Lu, Q. Wu and Y. Zhang, J. Chem. Phys., 140, 214117 (2014).

Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis

G. S. Sirin, Y. Zhang , J. Phys. Chem. A, 118,9132-9139 (2014)

How is Acetylcholinesterase Phosphonylated by Soman? An ab initio QM/MM Molecular Dynamics Study

Y. Shi, Y. Zhou, S. Wang, Y. Zhang , J. Phys. Chem. Lett., 4 , 491-495 (2013)

Sirtuin Deacetylation Mechanism and Catalytic Role of the Dynamic Cofactor Binding Loop

D. W. Rooklin, M. Lu, Y. Zhang , J. Am. Chem. Soc., 134, 15595-15603 (2012)

Revelation of a Catalytic Calcium-Binding Site Elucidates Unusual Metal Dependence of a Human Apyrase

Y. Zhou, S. M. Moin, S. Urban, Y. Zhang , Structure, 20, 1255-1263 (2012)

An Internal Water Retention Site in the Rhomboid Intramembrane Protease GlpG Ensures Catalytic Efficiency

Z. Lu, N. Zhou, Q. Wu, Y. Zhang, J. Chem. Theory Comput.,7, 4038-4049 (2011).

Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development

R. Wu, Z. Lu, Z. Cao and Y. Zhang, J. Am. Chem. Soc., 133, 6110-6113 (2011).

Zinc Chelation with Hydroxamate in Histone Deacetylases Modulated by Water Access to the Linker Binding Channel

National Science Foundation Career Award (2005), James D. Watson Young Investigator Award (2005), Whitehead Fellowship for Junior Faculty in Biomedical and Biological Sciences (2006)

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