Current Status of the AMOEBA Polarizable Force Field.
J. Ponder, C. Wu, V. S. Pande, I. Haque, R. A. Distasio Jr., D. Lambrecht, M. Head-Gordon, G. Clark, M. Johnson, and T. Head-Gordon. J. Phys. Chem. B., 114 2549-2564…
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Unfolded state dynamics and structure of protein L characterized by simulation and experiment.
V. Voelz, V. Singh, W. J. Wedemeyer, L. Lapidus, and V. S. Pande. Journal of the ACS, 132 4702–4709 (2010) ABSTRACT. While several experimental techniques now exist for characterizing protein…
Read moreNetwork models for molecular kinetics and their initial applications to human health.
G. Bowman, X. Huang, and V. S. Pande. Cell Research 20 622-630 (2010) ABSTRACT. Molecular kinetics underlies all biological phenomena and, like many other biological processes, may best be understood…
Read moreWater Ordering at Membrane Interfaces Controls Fusion Dynamics
Peter M. Kasson, Erik Lindahl, and Vijay S. Pande. Journal of the American Chemical Society (2011) Epub 25 Feb. SUMMARY. Building on our previous simulations of membrane fusion, we have…
Read moreEquilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics
AJ DePaul, EJ Thompson, SS Patel, K Haldeman & EJ Sorin. Nucleic Acids Research (2010) 38, 4856-4867 (Featured Cover Article) SUMMARY. We continue to study a small but ubiquitous RNA…
Read moreEvaluating Molecular Mechanical Potentials for Helical Peptides and Proteins.
EJ Thompson, AJ DePaul, SS Patel & EJ Sorin. PLoS ONE (2010) 5, e10056 SUMMARY. Our assessment of biophysical force fields as applied to helical peptides and proteins continues with…
Read moreA simple theory of protein folding kinetics.
V. S. Pande. Physical Review Letters (2010). SUMMARY. Recent work from detailed simulations of protein folding resulting from Folding@home have suggested some surprises and radical changes in how one conceptualizes…
Read moreProtein 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…
Read moreAtomic-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…
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