Zhang, Yingkai - New York University - Department of Chemistry

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. 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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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 L. Lior-Hoffmann, S. Ding, N. E. Geacintov, Y. Zhang and S. Broyde, Biochemistry, 53, 5683-5691 (2014).Structural and Dynamic Characterization of Polymerase k's Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity 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. Cai, H. Zheng, S. Ding, K. Kropachev, A. G. Schwaid, Y. Tang, H. Mu, S. Wang, N. Geacintov, Y. Zhang and S. Broyde,Chem. Res. Toxicol, 26, 1115-1125 (2013). Free Energy Profiles of Base Flipping in Intercalative Polycyclic Aromatic Hydrocarbon-Damaged DNA Duplexes: Energetic and Structural Relationships to Nucleotide Excision Repair Susceptibility J. Yang, L. Lior-Hoffmann, S. Wang, Y. Zhang , and S. Broyde, Biochemistry, 52, 2828-2838 (2013)DNA cytosine methylation: Structural and thermodynamic characterization of the epigenetic marking mechanism 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 G. S. Sirin, Y. Zhou,L. Lior-Hoffmann, S. Wang, Y. Zhang , J. Phys. Chem. B, 116, 12199-12207 (2012)Aging Mechanism of Soman Inhibited Acetylcholinesterase 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 L. Lior-Hoffmann, L. Wang, S. Wang, N. Geacintov, S. Broyde and Y. Zhang , Nucleic Acids Res., 40, 9193-9205 (2012)Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase k elucidates error-free bypass of a bulky DNA lesion 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 R. Wu, Z. Cao, Y. Zhang Progress in Chemistry, 24,1175-1184 (2012)Computational Simulations of Zinc Enzyme: Challenges and Recent Advances R. Wu, W. Gong, T. Liu, Y. Zhang and Z. Cao, J. Phys. Chem. B, 116, 1984-1991 (2012)QM/MM Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase 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 Z. Ke, G. Smith, Y. Zhang and H. Guo, J. Am. Chem. Soc., 133, 11103-11105 (2011)Molecular Mechanism for Eliminylation, a Newly Discovered Post-Translational Modification 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 Z. Ke, H. Guo, D. Xie, S. Wang and Y. Zhang, J. Phys. Chem. B, 115, 3725-3733, (2011).Ab Initio QM/MM Free-Energy Studies of Arginine Deiminase Catalysis: The Protonation State of the Cys Nucleophile. R. Wu, Z. Lu, Z. Cao and Y. Zhang, J. Chem. Theory Comput., 7, 433-443 (2011).A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins