Jerry M. Parks Ph.D.

Publications

7. Mechanism of Hg-C protonolysis in the bacterial organomercurial lyase MerB, J. M. Parks, H. Guo, C. Momany, L. Liang, S. M. Miller, A. O. Summers, and J. C. Smith, J. Am. Chem. Soc., 2009, 131, 13278-13285.

http://pubs.acs.org/doi/pdf/10.1021/ja9016123

6. Mechanism of Cdc25b phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculations, J. M. Parks, H. Hu, J. Rudolph, and W.T. Yang, J. Phys. Chem. B, 2009, 113 (15), 5217-5224.

http://dx.doi.org/10.1021/jp805137x

5. A pseudobond parameterization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes, J. M. Parks, H. Hu, A. J. Cohen and W.T. Yang, J. Chem. Phys., 2008, 129, 154106.

http://link.aip.org/link/?JCPSA6/129/154106/1

4. Hepatitis C virus NS5b polymerase: QM/MM calculations show the important roles of the internal energy in ligand binding, J. M. Parks, R. K. Kondru, H. Hu, D. N. Beratan, and W.T. Yang, J. Phys. Chem. B, 2008, 112 (10), 3168-3176.

http://dx.doi.org/10.1021/jp076885j

3. QM/MM Minimum Free Energy Path for accurate reaction energetics in solution and enzymes: Iterative optimization on the potential of mean force surface, H. Hu, Z.Y. Lu, J. M. Parks, S. K. Burger, W.T. Yang, J. Chem. Phys., 2008, 128, 034105.

http://link.aip.org/link/?JCPSA6/128/034105/1

2. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate,  J. Sohn, J. M. Parks, G. Buhrman, P. Brown, K. Kristjansdottir, A. Safi, H. Edelsbrunner, W.T. Yang, and J. Rudolph, Biochem., 2005, 44, 16563-16573.

http://dx.doi.org/10.1021/bi0516879

1. Quantum chemical characterization of the reactions of the phenylnitrenium ion with guanine, J. M. Parks, G. P. Ford and C. J. Cramer, J. Org. Chem., 2001, 66, 8997-9004.

http://dx.doi.org/10.1021/jo016066+