Deng NJ - Search Results

1

How long does it take to equilibrate the unfolded state of a protein?

Levy RM, Dai W, Deng NJ, Makarov DE. Levy RM, et al. Among authors: deng nj. Protein Sci. 2013 Nov;22(11):1459-65. doi: 10.1002/pro.2335. Epub 2013 Sep 17. Protein Sci. 2013. PMID: 23963761 Free PMC article.

2

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

Zheng W, Gallicchio E, Deng N, Andrec M, Levy RM. Zheng W, et al. J Phys Chem B. 2011 Feb 17;115(6):1512-23. doi: 10.1021/jp1089596. Epub 2011 Jan 21. J Phys Chem B. 2011. PMID: 21254767 Free PMC article.

3

Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations.

Deng NJ, Zheng W, Gallicchio E, Levy RM. Deng NJ, et al. J Am Chem Soc. 2011 Jun 22;133(24):9387-94. doi: 10.1021/ja2008032. Epub 2011 May 25. J Am Chem Soc. 2011. PMID: 21561098 Free PMC article.

4

NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations.

Xia J, Deng NJ, Levy RM. Xia J, et al. Among authors: deng nj. J Phys Chem B. 2013 Jun 6;117(22):6625-34. doi: 10.1021/jp400797y. Epub 2013 May 28. J Phys Chem B. 2013. PMID: 23638941 Free PMC article.

5

How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory.

Deng NJ, Dai W, Levy RM. Deng NJ, et al. J Phys Chem B. 2013 Oct 24;117(42):12787-99. doi: 10.1021/jp401962k. Epub 2013 Jun 13. J Phys Chem B. 2013. PMID: 23705683 Free PMC article.

6

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.

Gallicchio E, Deng N, He P, Wickstrom L, Perryman AL, Santiago DN, Forli S, Olson AJ, Levy RM. Gallicchio E, et al. J Comput Aided Mol Des. 2014 Apr;28(4):475-90. doi: 10.1007/s10822-014-9711-9. Epub 2014 Feb 7. J Comput Aided Mol Des. 2014. PMID: 24504704 Free PMC article.

7

Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease.

Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM. Deng N, et al. J Phys Chem B. 2015 Jan 22;119(3):976-88. doi: 10.1021/jp506376z. Epub 2014 Sep 17. J Phys Chem B. 2015. PMID: 25189630 Free PMC article.

8

The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase.

Slaughter A, Jurado KA, Deng N, Feng L, Kessl JJ, Shkriabai N, Larue RC, Fadel HJ, Patel PA, Jena N, Fuchs JR, Poeschla E, Levy RM, Engelman A, Kvaratskhelia M. Slaughter A, et al. Retrovirology. 2014 Nov 25;11:100. doi: 10.1186/s12977-014-0100-1. Retrovirology. 2014. PMID: 25421939 Free PMC article.

9

Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

Deng N, Zhang BW, Levy RM. Deng N, et al. J Chem Theory Comput. 2015 Jun 9;11(6):2868-78. doi: 10.1021/acs.jctc.5b00264. J Chem Theory Comput. 2015. PMID: 26236174 Free PMC article.

10

Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.

Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Wickstrom L, et al. J Mol Recognit. 2016 Jan;29(1):10-21. doi: 10.1002/jmr.2489. Epub 2015 Aug 10. J Mol Recognit. 2016. PMID: 26256816 Free PMC article.

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