Protein folded states are kinetic hubs.
G. R. Bowman and V. S. Pande. Proceedings of the National Academy of Sciences, USA (2010). SUMMARY. By analyzing recent results from Folding@home, we have found a set of general…
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Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails.
P. M. Kasson, E. Lindahl, and V. S. Pande. PLoS Computational Biology 6(6): e1000829 (2010). SUMMARY. Membrane fusion is a common underlying process critical to neurotransmitter release, cellular trafficking, and…
Read moreMolecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
Voelz VA, Bowman GR, Beauchamp K, Pande VS. Journal of the American Chemical Society (2010) SUMMARY. Simulating protein folding on the millisecond timescale has been a major challenge for many…
Read moreBayesian comparison of Markov models of molecular dynamics with detailed balance constraint
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 moreCombining Molecular Dynamics with Bayesian Analysis To Predict and Evaluate Ligand-Binding Mutations in Influenza Hemagglutinin.
P. 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 moreThe Roles of Entropy and Kinetics in Structure Prediction.
G. 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 moreUsing generalized ensemble simulations and Markov state models to identify conformational states.
G. 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 moreFolding@home: lessons from eight years of distributed computing.
A. 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 moreProbing the nanosecond dynamics of a designed three-stranded beta-sheet with massively parallel molecular dynamics simulation.
V. 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 moreA multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel.
Vincent 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…
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