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Elizabeth J. Denning, Ph.D.

Affiliations: 
2009 Johns Hopkins University, Baltimore, MD 
Area:
General Biophysics
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Jan H. Hoh grad student 2009 Johns Hopkins
 (Computer simulations used to understand the roles of voltage and domain motions during potassium channel gating.)

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Publications

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Stennett EM, Dotson DL, Denning EJ, et al. (2014) Investigating the Conformational Dynamics of DNA with Lesions through Fluorescence-Based Technniques and Computer Simulations Biophysical Journal. 106: 68a
Denning EJ, Thirumalai D, MacKerell AD. (2013) Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure. Biophysical Chemistry. 184: 8-16
McDonald AR, Denning EJ, MacKerell AD. (2013) Impact of geometry optimization on base-base stacking interaction energies in the canonical A- and B-forms of DNA. The Journal of Physical Chemistry. A. 117: 1560-8
Denning E, MacKerell AD. (2013) Impact of Osmolytes on the RNA Hairpin as Studied using Molecular Dynamics Simulations Biophysical Journal. 104
Hart K, Foloppe N, Baker CM, et al. (2012) Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. Journal of Chemical Theory and Computation. 8: 348-362
Denning EJ, MacKerell AD. (2012) Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity. Journal of the American Chemical Society. 134: 2800-6
Denning E, Thirumalai D, MacKerell AD. (2012) Impact of TMAO on the preQ1 RNA Riboswitch Studied using Molecular Dynamics Simulations Biophysical Journal. 102
Michaud-Agrawal N, Denning EJ, Woolf TB, et al. (2011) MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry. 32: 2319-27
Denning EJ, Priyakumar UD, Nilsson L, et al. (2011) Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. Journal of Computational Chemistry. 32: 1929-43
Perilla JR, Beckstein O, Denning EJ, et al. (2011) Computing ensembles of transitions from stable states: Dynamic importance sampling. Journal of Computational Chemistry. 32: 196-209
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