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Elizabeth J. Denning, Ph.D. - Publications

Affiliations: 
2009 Johns Hopkins University, Baltimore, MD 
Area:
General Biophysics
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17 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2014 Stennett EM, Dotson DL, Denning EJ, Beckstein O, Levitus M. Investigating the Conformational Dynamics of DNA with Lesions through Fluorescence-Based Technniques and Computer Simulations Biophysical Journal. 106: 68a. DOI: 10.1016/J.Bpj.2013.11.455  0.362
2013 Denning EJ, Thirumalai D, MacKerell AD. Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure. Biophysical Chemistry. 184: 8-16. PMID 24012912 DOI: 10.1016/J.Bpc.2013.08.002  0.413
2013 McDonald AR, Denning EJ, MacKerell AD. 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. PMID 23343365 DOI: 10.1021/Jp308364D  0.329
2013 Denning E, MacKerell AD. Impact of Osmolytes on the RNA Hairpin as Studied using Molecular Dynamics Simulations Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.1478  0.443
2012 Hart K, Foloppe N, Baker CM, Denning EJ, Nilsson L, Mackerell AD. 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. PMID 22368531 DOI: 10.1021/Ct200723Y  0.373
2012 Denning EJ, MacKerell AD. Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity. Journal of the American Chemical Society. 134: 2800-6. PMID 22242623 DOI: 10.1021/Ja211328G  0.415
2012 Denning E, Thirumalai D, MacKerell AD. Impact of TMAO on the preQ1 RNA Riboswitch Studied using Molecular Dynamics Simulations Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.1529  0.44
2011 Michaud-Agrawal N, Denning EJ, Woolf TB, Beckstein O. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry. 32: 2319-27. PMID 21500218 DOI: 10.1002/Jcc.21787  0.335
2011 Denning EJ, Priyakumar UD, Nilsson L, Mackerell AD. 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. PMID 21469161 DOI: 10.1002/Jcc.21777  0.434
2011 Perilla JR, Beckstein O, Denning EJ, Woolf TB. Computing ensembles of transitions from stable states: Dynamic importance sampling. Journal of Computational Chemistry. 32: 196-209. PMID 21132840 DOI: 10.1002/Jcc.21564  0.37
2011 Denning E, Priyakumar UD, MacKerell AD. Relationship of the 2′-Hydroxyl Orientation in RNA to Watson-Crick Base Pair Opening Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.3526  0.371
2010 Denning EJ, Woolf TB. Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations. Proteins. 78: 1105-19. PMID 19950367 DOI: 10.1002/Prot.22632  0.379
2009 Denning EJ, Crozier PS, Sachs JN, Woolf TB. From the gating charge response to pore domain movement: initial motions of Kv1.2 dynamics under physiological voltage changes. Molecular Membrane Biology. 26: 397-421. PMID 19883299 DOI: 10.3109/09687680903278539  0.329
2009 Beckstein O, Denning EJ, Perilla JR, Woolf TB. Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions. Journal of Molecular Biology. 394: 160-76. PMID 19751742 DOI: 10.1016/J.Jmb.2009.09.009  0.411
2009 Denning E, Woolf T. Understanding gating transitions within K+ channels using Dynamic Importance Sampling Biophysical Journal. 96: 192a. DOI: 10.1016/J.Bpj.2008.12.902  0.366
2009 Beckstein O, Denning EJ, Woolf TB. The Closed <-> Open Transition of Adenylate Kinase From Crystal Structures and Computer Simulations Biophysical Journal. 96: 70a-71a. DOI: 10.1016/J.Bpj.2008.12.264  0.361
2008 Denning EJ, Woolf TB. Double bilayers and transmembrane gradients: a molecular dynamics study of a highly charged peptide. Biophysical Journal. 95: 3161-73. PMID 18586841 DOI: 10.1529/Biophysj.108.134049  0.301
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