molecular dynamics

Substrate-to-product conversion facilitates active site loop opening in yeast enolase: A molecular dynamics study

262. P. Li and S. Hammes-Schiffer, “Substrate-to-product conversion facilitates active site loop opening in yeast enolase: A molecular dynamics study,” ACS Catal. 9, 8985-8990 (2019).

Effects of Active Site Mutations on Specificity of Nucleobase Binding in Human DNA Polymerase η

223. M. N. Ucisik and S. Hammes-Schiffer, “Effects of active site mutations on specificity of nucleobase binding in human DNA polymerase η,” J. Phys. Chem. B 121, 3667-3675 (2017).

Assessing the potential effects of active site Mg2+ ions in the glmS ribozyme-cofactor complex

194. S. Zhang, D. R. Stevens, P. Goyal, J. L. Bingaman, P. C. Bevilacqua, and S. Hammes-Schiffer, “Assessing the potential effects of active site Mg2+ ions in the glmS ribozyme-cofactor complex,” J. Phys. Chem. Lett. 7, 3984-3988 (2016).

Molecular Dynamics Study of Twister Ribozyme: Role of Mg2+ Ions and the Hydrogen-Bonding Network in the Active Site

210. M. N. Ucisik, P. C. Bevilacqua, and S. Hammes-Schiffer, “Molecular dynamics study of twister ribozyme: Role of Mg2+ ions and the hydrogen-bonding network in the active site,” Biochemistry. 55, 3834-3846 (2016).

Comparative molecular dynamics studies of human DNA polymerase η

199. M. N. Ucisik and S. Hammes-Schiffer, “Comparative molecular dynamics studies of human DNA polymerase η,” J. Chem. Inf. Model. 55, 2672-2681 (2015).

Long distance communication in the HDV ribozyme: Insights from molecular dynamics and experiments

129. N. Veeraraghavan, P. C. Bevilacqua, and S. Hammes-Schiffer, “Long distance communication in the HDV ribozyme: Insights from molecular dynamics and experiments,” J. Mol. Biol. 402, 278-291 (2010).

Impact of mutation on proton transfer reactions in ketosteroid isomerase: Insights from molecular dynamics simulations.

127. D.K. Chakravorty and S. Hammes-Schiffer, “Impact of mutation on proton transfer reactions in ketosteroid isomerase: Insights from molecular dynamics simulations,” J. Am. Chem. Soc. 132, 7549-7555 (2010).

Molecular dynamics of excited state intramolecular proton transfer: 2-(2′-hydroxyphenyl)-4-methyloxazole in gas phase, solution and protein environments

65. O. Vendrell, M. Moreno, J. M. Lluch, and S. Hammes-Schiffer, “Molecular dynamics of excited state intramolecular proton transfer: 2-(2′-hydroxyphenyl)-4-methyloxazole in gas phase, solution and protein environments,” J. Phys. Chem. B 108, 6616-6623 (2004).

Molecular dynamics with quantum transitions for proton transfer: Quantum treatment of hydrogen and donor-acceptor motions

59. S. Y. Kim and S. Hammes-Schiffer, “Molecular dynamics with quantum transitions for proton transfer: Quantum treatment of hydrogen and donor-acceptor motions,” J. Chem. Phys. 119, 4389-4398 (2003).

Molecular dynamics simulation of proton-coupled electron transfer in solution

47. M. Kobrak and S. Hammes-Schiffer, “Molecular dynamics simulation of proton-coupled electron transfer in solution,” J. Phys. Chem. B 105, 10435-10445 (2001).