The 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…
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Using 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…
Read moreThe Fip35 WW Domain Folds with Structural and Mechanistic Heterogeneity in Molecular Dynamics Simulations.
D. 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 moreAccelerating Molecular Dynamic Simulation on Graphics Processing Units.
M. 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 moreThe predicted structure of the headpiece of the Huntingtin protein and its implications on Huntington aggregation
Nicholas 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…
Read moreCombining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin.
Peter M. Kasson and Vijay S. Pande. Pacific Symposium on Biocomputing 14:492-503(2009). SUMMARY. The influenza hemagglutinin protein performs several important functions, including attaching the virus to cells it will infect…
Read moreAccelerating Molecular Dynamic Simulation on the Cell processor and PlayStation 3
Edgar Luttmann, Daniel L. Ensign, Vishal Vaidyanathan, Mike Houston, Noam Rimon, Jeppe Øland, Guha Jayachandran, Mark Friedrichs, Vijay S. Pande. Journal of Computational Chemistry (2009) SUMMARY. In this paper, we…
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