S. Bacallado, J. Chodera, and V. Pande. Journal of Chemical Physics 131, 045106 (2009). SUMMARY. Markov State Models (MSMs) are one of the most common ways to analyze Folding@Home simulations.…
Read moreP. M. Kasson, D. L. Ensign, and V. S. Pande. Journal of the American Chemical Society (2009). Published online 2009 July 28. SUMMARY. The influenza virus infects people and animals…
Read moreG. R. Bowman and V. S. Pande. PLoS ONE 4(6): e5840 (2009) ABSTRACT. Here we continue our efforts to use methods developed in the folding mechanism community to both better…
Read moreG. R. Bowman, X. Huang, and V. S. Pande. Methods 49(2): 197-201 (2009) ABSTRACT Part of understanding a molecule’s conformational dynamics is mapping out the dominant metastable, or long lived,…
Read moreA. Beberg and V. S. Pande. ipdps, pp.1-8, IEEE International Symposium on Parallel & Distributed Processing (2009) ABSTRACT Accurate simulation of biophysical processes requires vast computing resources. Folding@home is a…
Read moreV. A. Voelz, E. Luttmann, G. R. Bowman, and V.S. Pande. International Journal of Molecular Sciences 10(3): 1013 (2009) ABSTRACT Recently a temperature-jump FTIR study of a designed three-stranded sheet…
Read moreVincent A. Voelz, Paula Petrone and Vijay S. Pande. Pacific Symposium on Biocomputing, 14:340-352 (2009) ABSTRACT We present a new multiscale method that combines all-atom molecular dy- namics with coarse-grained…
Read moreD. L. Ensign and V. S. Pande. Biophysical Journal 96 L53-55 (2009) ABSTRACT. We describe molecular dynamics simulations resulting in the folding the Fip35 Hpin1 WW domain. The simulations were…
Read moreM. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande. J. Comp. Chem., (2009) SUMMARY. This paper…
Read moreNicholas W. Kelley, Xuhui Huang, Stephen Tam, Christoph Spiess, Judith Frydman and Vijay S. Pande. Journal of Molecular Biology (2009) SUMMARY. The aggregation of the Huntingtin (Htt) protein has been…
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