Simulating protein folding on the millisecond timescale has been a major challenge for many years. When we started Folding@home, our first goal was to break the microsecond barrier. This barrier is 1000x fold harder and represents a major step forward in molecular simulation.
Specifically, in a recent paper (http://pubs.acs.org/doi/abs/10.1021/ja9090353), Folding@home researchers Vincent Voelz, Greg Bowman, Kyle Beauchamp, and Vijay Pande have broken this barrier. The movie below is of one of the trajectories that folded (i.e. started unfolded and ended up in the folded state). From simulations like these, we have found some new surprises in how proteins fold. Please see the paper (url above) for more details.
Why is this important? This is important since protein misfolding occurs on long timescales and this first simulation on the millisecond simulation for protein folding means we have demonstrated our new Markov State Model (MSM) technology can successfully simulate very long timescales. It make sense to go after protein folding first, since there is a wealth of experimental data for us to test our simulations.
While this paper on protein folding has just come out, we have already been using this MSM technology to study protein misfolding in Alzheimer's Disease, following up from our 2008 paper. While our previous paper was able to get to long enough timescales to see small molecular weight oligomers, this new methodology gives us hope to push further with our simulations of Alzheimer's, making more direct connections to larger, more complex Abeta oligomers than we were previously able to do.