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Author: Viktor

Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide.

October 4, 2006 by Viktor

P. Kasson and V. S. Pande. PSB, (2006) SUMMARY: We have been applying Folding@home to study the nature of key proteins involved in how flu (the influenza virus) gains access…

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A Bayesian Update Method for Adaptive Weighted Sampling.

October 4, 2006 by Viktor

S. Park and V. S. Pande. Physical Review E (2006) SUMMARY: We’ve developed a new way to do a particular type of calculation (for protein thermodynamics) on Folding@home. This paper…

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Local structure formation in simulations of two small proteins.

October 4, 2006 by Viktor

Guha Jayachandran, V. Vishal, Angel E. Garcıa and V. S. Pande. Journal of Structural Biology, (2006) Local PDF ABSTRACT: Massively parallel all-atom, explicit solvent molecular dynamics simulations were used to…

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Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates.

October 4, 2006 by Viktor

C. Snow and V. S. Pande. Biophysical Journal, (2006) ABSTRACT: Using distributed molecular dynamics simulations we located 4 distinct folding transitions for a 39 residue beta-beta-alpha-beta protein fold. We introduce…

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Parallelized Over Parts Computation of Absolute Binding Free Energy with Docking and Molecular Dynamics.

October 4, 2006 by Viktor

Guha Jayachandran, M. R. Shirts, S. Park, and V. S. Pande. Journal of Chemical Physics, (2006) ABSTRACT: We present a technique for biomolecular free energy calculations that exploits highly parallelized…

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Folding Simulations of the Villin Headpiece in All-Atom Detail.

October 4, 2006 by Viktor

Guha Jayachandran, V. Vishal, and V. S. Pande. Journal of Chemical Physics (2006) SUMMARY: We have developed a new method which greatly extends Folding@home’s ability to simulate long timescales. This…

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Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion

October 4, 2006 by Viktor

P. Kasson, N. Kelley, N. Singhal, M. Vrjlic, A. Brunger, and V. S. Pande. Proceedings of the National Academy of Sciences, USA SUMMARY: These first results describe work we’ve been…

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Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory.

October 4, 2006 by Viktor

Ian T. Suydam, Christopher D. Snow, Vijay S. Pande, Steven G. Boxer. Science (2006) Full Text SUMMARY: The ability to quantitatively predict electric fields in proteins has remained a great…

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Kinetic Computational Alanine Scanning: Application to p53 Oligomerization

October 4, 2006 by Viktor

L.T. Chong, W. C. Swope, J. W. Pitera, and V. S. Pande. Journal of Molecular Biology (2006) SUMMARY: Roughly half of all known cancers involve a mutation in a single…

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Validation of Markov state models using Shannon’s entropy.

October 4, 2006 by Viktor

S. Park and V. S. Pande. Journal of Chemical Physics (2006) SUMMARY: Markov State Models (MSM’s) have become a major part of how Folding@home calculations are performed. In particular, the…

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