Levy RM - Search Results

1

A Stochastic Solution to the Unbinned WHAM Equations.

Zhang BW, Xia J, Tan Z, Levy RM. Zhang BW, et al. Among authors: levy rm. J Phys Chem Lett. 2015 Oct 1;6(19):3834-40. doi: 10.1021/acs.jpclett.5b01771. Epub 2015 Sep 14. J Phys Chem Lett. 2015. PMID: 26722879 Free PMC article.

2

Temperature weighted histogram analysis method, replica exchange, and transition paths.

Gallicchio E, Andrec M, Felts AK, Levy RM. Gallicchio E, et al. Among authors: levy rm. J Phys Chem B. 2005 Apr 14;109(14):6722-31. doi: 10.1021/jp045294f. J Phys Chem B. 2005. PMID: 16851756

3

Simple continuous and discrete models for simulating replica exchange simulations of protein folding.

Zheng W, Andrec M, Gallicchio E, Levy RM. Zheng W, et al. Among authors: levy rm. J Phys Chem B. 2008 May 15;112(19):6083-93. doi: 10.1021/jp076377+. Epub 2008 Feb 6. J Phys Chem B. 2008. PMID: 18251533 Free PMC article.

4

Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics.

Zheng W, Andrec M, Gallicchio E, Levy RM. Zheng W, et al. Among authors: levy rm. J Phys Chem B. 2009 Aug 27;113(34):11702-9. doi: 10.1021/jp900445t. J Phys Chem B. 2009. PMID: 19655770 Free PMC article.

5

Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting.

Okumura H, Gallicchio E, Levy RM. Okumura H, et al. Among authors: levy rm. J Comput Chem. 2010 May;31(7):1357-67. doi: 10.1002/jcc.21419. J Comput Chem. 2010. PMID: 19882731 Free PMC article.

6

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. Among authors: levy rm. 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.

7

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. Among authors: levy rm. 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.

8

Theory of binless multi-state free energy estimation with applications to protein-ligand binding.

Tan Z, Gallicchio E, Lapelosa M, Levy RM. Tan Z, et al. Among authors: levy rm. J Chem Phys. 2012 Apr 14;136(14):144102. doi: 10.1063/1.3701175. J Chem Phys. 2012. PMID: 22502496 Free PMC article.

9

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: levy rm. 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.

10

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. Among authors: levy rm. 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.

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