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Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39).
Voelz VA, Bowman GR, Beauchamp K, Pande VS. Voelz VA, et al. J Am Chem Soc. 2010 Feb 10;132(5):1526-8. doi: 10.1021/ja9090353. J Am Chem Soc. 2010. PMID: 20070076 Free PMC article.
Atomistic folding simulations of the five-helix bundle protein λ(6−85).
Bowman GR, Voelz VA, Pande VS. Bowman GR, et al. J Am Chem Soc. 2011 Feb 2;133(4):664-7. doi: 10.1021/ja106936n. J Am Chem Soc. 2011. PMID: 21174461 Free PMC article.
Markov state model reveals folding and functional dynamics in ultra-long MD trajectories.
Lane TJ, Bowman GR, Beauchamp K, Voelz VA, Pande VS. Lane TJ, et al. J Am Chem Soc. 2011 Nov 16;133(45):18413-9. doi: 10.1021/ja207470h. Epub 2011 Oct 26. J Am Chem Soc. 2011. PMID: 21988563 Free PMC article.
Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment.
Voelz VA, Jäger M, Yao S, Chen Y, Zhu L, Waldauer SA, Bowman GR, Friedrichs M, Bakajin O, Lapidus LJ, Weiss S, Pande VS. Voelz VA, et al. J Am Chem Soc. 2012 Aug 1;134(30):12565-77. doi: 10.1021/ja302528z. Epub 2012 Jul 19. J Am Chem Soc. 2012. PMID: 22747188 Free PMC article.
A molecular interpretation of 2D IR protein folding experiments with Markov state models.
Baiz CR, Lin YS, Peng CS, Beauchamp KA, Voelz VA, Pande VS, Tokmakoff A. Baiz CR, et al. Biophys J. 2014 Mar 18;106(6):1359-70. doi: 10.1016/j.bpj.2014.02.008. Biophys J. 2014. PMID: 24655511 Free PMC article.
Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides.
Wakefield AE, Wuest WM, Voelz VA. Wakefield AE, et al. J Chem Inf Model. 2015 Apr 27;55(4):806-13. doi: 10.1021/ci500768u. Epub 2015 Mar 20. J Chem Inf Model. 2015. PMID: 25741627
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