Denning EJ - Search Results

1

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

Denning EJ, Priyakumar UD, Nilsson L, Mackerell AD Jr. Denning EJ, et al. J Comput Chem. 2011 Jul 15;32(9):1929-43. doi: 10.1002/jcc.21777. Epub 2011 Apr 5. J Comput Chem. 2011. PMID: 21469161 Free PMC article.

2

Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity.

Denning EJ, MacKerell AD Jr. Denning EJ, et al. J Am Chem Soc. 2012 Feb 8;134(5):2800-6. doi: 10.1021/ja211328g. Epub 2012 Jan 27. J Am Chem Soc. 2012. PMID: 22242623 Free PMC article.

3

Impact of geometry optimization on base-base stacking interaction energies in the canonical A- and B-forms of DNA.

McDonald AR, Denning EJ, MacKerell AD Jr. McDonald AR, et al. Among authors: denning ej. J Phys Chem A. 2013 Feb 21;117(7):1560-8. doi: 10.1021/jp308364d. Epub 2013 Feb 12. J Phys Chem A. 2013. PMID: 23343365 Free PMC article.

4

Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure.

Denning EJ, Thirumalai D, MacKerell AD Jr. Denning EJ, et al. Biophys Chem. 2013 Dec 31;184:8-16. doi: 10.1016/j.bpc.2013.08.002. Epub 2013 Aug 17. Biophys Chem. 2013. PMID: 24012912 Free PMC article.

5

Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations.

Denning EJ, Mackerell AD Jr. Denning EJ, et al. J Am Chem Soc. 2011 Apr 20;133(15):5770-2. doi: 10.1021/ja201213b. Epub 2011 Mar 28. J Am Chem Soc. 2011. PMID: 21443192 Free PMC article.

6

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

Hart K, Foloppe N, Baker CM, Denning EJ, Nilsson L, Mackerell AD Jr. Hart K, et al. Among authors: denning ej. J Chem Theory Comput. 2012 Jan 10;8(1):348-362. doi: 10.1021/ct200723y. J Chem Theory Comput. 2012. PMID: 22368531 Free PMC article.

7

Computing ensembles of transitions from stable states: Dynamic importance sampling.

Perilla JR, Beckstein O, Denning EJ, Woolf TB. Perilla JR, et al. Among authors: denning ej. J Comput Chem. 2011 Jan 30;32(2):196-209. doi: 10.1002/jcc.21564. J Comput Chem. 2011. PMID: 21132840 Free PMC article.

8

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

Michaud-Agrawal N, Denning EJ, Woolf TB, Beckstein O. Michaud-Agrawal N, et al. Among authors: denning ej. J Comput Chem. 2011 Jul 30;32(10):2319-27. doi: 10.1002/jcc.21787. Epub 2011 Apr 15. J Comput Chem. 2011. PMID: 21500218 Free PMC article.

9

Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations.

Denning EJ, Woolf TB. Denning EJ, et al. Proteins. 2010 Apr;78(5):1105-19. doi: 10.1002/prot.22632. Proteins. 2010. PMID: 19950367 Free PMC article.

10

Influence of lipids on protein-mediated transmembrane transport.

Denning EJ, Beckstein O. Denning EJ, et al. Chem Phys Lipids. 2013 Apr;169:57-71. doi: 10.1016/j.chemphyslip.2013.02.007. Epub 2013 Mar 6. Chem Phys Lipids. 2013. PMID: 23473882 Review.

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