molecular dynamics

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).

Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics simulations of hydrogen transfer reactions in enzymes

41. S. R. Billeter, S. P. Webb, T. Iordanov, P. K. Agarwal, and S. Hammes-Schiffer, “Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics simulations of hydrogen transfer reactions in enzymes,” J. Chem. Phys. 114, 6925-6936 (2001).