Protein folding under confinement: a role for solvent.
D. Lucent, V. Vishal, V. S. Pande. Proceedings of the National Academy of Sciences (2007) Local PDF SUMMARY: When proteins fold inside a cell, they are frequently subjected to various…
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Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.
J. Chodera, N. Singhal, V. S. Pande, K. Dill, and W. Swope. Journal of Chemical Physics, (2007) SUMMARY: In order to break up calculations to run on Folding@home and then…
Read moreStorage@home: Petascale Distributed Storage
Adam L Beberg and Vijay S. Pande. IPDPS (2007) SUMMARY: Storage@home is a distributed storage infrastructure developed to solve the problem of backing up and sharing petabytes of scientific results…
Read moreN-Body simulation on GPUs
Erich Elsen, Mike Houston, V. Vishal, Eric Darve, Pat Hanrahan, and Vijay Pande. Proceedings of the 2006 ACM/IEEE conference on Supercomputing (2006). SUMMARY. This paper details our first efforts with…
Read morePredicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide.
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…
Read moreA Bayesian Update Method for Adaptive Weighted Sampling.
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…
Read moreLocal structure formation in simulations of two small proteins.
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…
Read moreKinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates.
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…
Read moreParallelized Over Parts Computation of Absolute Binding Free Energy with Docking and Molecular Dynamics.
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…
Read moreFolding Simulations of the Villin Headpiece in All-Atom Detail.
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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