SMP code development making progress
Peter has been making great progress with the SMP client. We haven’t been talking about SMP client development much, but there has been a lot going on behind the scenes. …
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Why the new blog?
PS People have asked me why the new site (instead of our old site on the foldingathome.org/news.html page). The main idea is that I’ve been wanting to get new features…
Read moreA crazy day/night
There was a major network outage yesterday at Stanford yesterday: At 11:45 a.m. today, a contractor cut a cable to Forsythe Hall resulting in a disruption of university computer service. …
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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