Zhang Y - Search Results

1

Aging mechanism of soman inhibited acetylcholinesterase.

Sirin GS, Zhou Y, Lior-Hoffmann L, Wang S, Zhang Y. Sirin GS, et al. Among authors: zhang y. J Phys Chem B. 2012 Oct 11;116(40):12199-207. doi: 10.1021/jp307790v. Epub 2012 Sep 28. J Phys Chem B. 2012. PMID: 22984913 Free PMC article.

2

Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.

Wang S, Hu P, Zhang Y. Wang S, et al. Among authors: zhang y. J Phys Chem B. 2007 Apr 12;111(14):3758-64. doi: 10.1021/jp067147i. Epub 2007 Mar 22. J Phys Chem B. 2007. PMID: 17388541 Free PMC article.

3

Catalytic mechanism and metal specificity of bacterial peptide deformylase: a density functional theory QM/MM study.

Xiao C, Zhang Y. Xiao C, et al. Among authors: zhang y. J Phys Chem B. 2007 Jun 7;111(22):6229-35. doi: 10.1021/jp068657f. Epub 2007 May 16. J Phys Chem B. 2007. PMID: 17503802

4

How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations.

Hu P, Wang S, Zhang Y. Hu P, et al. Among authors: zhang y. J Am Chem Soc. 2008 Mar 26;130(12):3806-13. doi: 10.1021/ja075896n. Epub 2008 Mar 1. J Am Chem Soc. 2008. PMID: 18311969 Free PMC article.

5

Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations.

Hu P, Wang S, Zhang Y. Hu P, et al. Among authors: zhang y. J Am Chem Soc. 2008 Dec 10;130(49):16721-8. doi: 10.1021/ja807269j. J Am Chem Soc. 2008. PMID: 19049465 Free PMC article.

6

Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.

Zheng H, Wang S, Zhang Y. Zheng H, et al. Among authors: zhang y. J Comput Chem. 2009 Dec;30(16):2706-11. doi: 10.1002/jcc.21296. J Comput Chem. 2009. PMID: 19399770 Free PMC article.

7

Active site cysteine is protonated in the PAD4 Michaelis complex: evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.

Ke Z, Zhou Y, Hu P, Wang S, Xie D, Zhang Y. Ke Z, et al. Among authors: zhang y. J Phys Chem B. 2009 Sep 24;113(38):12750-8. doi: 10.1021/jp903173c. J Phys Chem B. 2009. PMID: 19507815 Free PMC article.

8

Reaction pathway and free-energy barrier for reactivation of dimethylphosphoryl-inhibited human acetylcholinesterase.

Liu J, Zhang Y, Zhan CG. Liu J, et al. Among authors: zhang y. J Phys Chem B. 2009 Dec 17;113(50):16226-36. doi: 10.1021/jp9055335. J Phys Chem B. 2009. PMID: 19924840 Free PMC article.

9

Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4.

Ke Z, Wang S, Xie D, Zhang Y. Ke Z, et al. Among authors: zhang y. J Phys Chem B. 2009 Dec 31;113(52):16705-10. doi: 10.1021/jp9080614. J Phys Chem B. 2009. PMID: 20028143 Free PMC article.

10

Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study.

Wu R, Hu P, Wang S, Cao Z, Zhang Y. Wu R, et al. Among authors: zhang y. J Chem Theory Comput. 2009 Dec 2;6(1):337. doi: 10.1021/ct9005322. J Chem Theory Comput. 2009. PMID: 20161624 Free PMC article.

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