Zhang Y - Search Results

1

Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: energetic and structural relationships to nucleotide excision repair susceptibility.

Cai Y, Zheng H, Ding S, Kropachev K, Schwaid AG, Tang Y, Mu H, Wang S, Geacintov NE, Zhang Y, Broyde S. Cai Y, et al. Among authors: zhang y. Chem Res Toxicol. 2013 Jul 15;26(7):1115-25. doi: 10.1021/tx400156a. Epub 2013 Jul 2. Chem Res Toxicol. 2013. PMID: 23758590 Free PMC article.

2

A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.

Wang L, Yu X, Hu P, Broyde S, Zhang Y. Wang L, et al. Among authors: zhang y. J Am Chem Soc. 2007 Apr 18;129(15):4731-7. doi: 10.1021/ja068821c. Epub 2007 Mar 22. J Am Chem Soc. 2007. PMID: 17375926 Free PMC article.

3

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.

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

Determination of free energy profiles by repository based adaptive umbrella sampling: bridging nonequilibrium and quasiequilibrium simulations.

Zheng H, Zhang Y. Zheng H, et al. Among authors: zhang y. J Chem Phys. 2008 May 28;128(20):204106. doi: 10.1063/1.2920476. J Chem Phys. 2008. PMID: 18513009 Free PMC article.

6

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.

7

Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase.

Wang L, Broyde S, Zhang Y. Wang L, et al. Among authors: zhang y. J Mol Biol. 2009 Jun 19;389(4):787-96. doi: 10.1016/j.jmb.2009.04.029. Epub 2009 Apr 21. J Mol Biol. 2009. PMID: 19389406 Free PMC article.

8

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.

9

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.

10

Importance of charge independent effects in readout of the trimethyllysine mark by HP1 chromodomain.

Lu Z, Lai J, Zhang Y. Lu Z, et al. Among authors: zhang y. J Am Chem Soc. 2009 Oct 21;131(41):14928-31. doi: 10.1021/ja904951t. J Am Chem Soc. 2009. PMID: 19788305 Free PMC article.

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