Again, I am assuming that is what they are doing. I may be way off.
What this particular project is doing is attempting to simulate the various steps involved in the folding of specific, known proteins. By starting with an initial protein in pre-fold state, various algorithms are applied that predict different possibilities and paths for interaction between the molecules within the protein. The results (from a WU) are then used to generate the next potential step in the folding sequence (thus the F@H requirement that WUs be returned within a certain number of days, as the results of one WU would be used to generate the next one, as part of the sequence). The idea is that by knowing how particular proteins fold, one might be able to determine what internal and/or external factors could cause a protein to "mis-fold", as is the case with a number of diseases such as BSE (Bovine Spongiform Encephalopathy or "Mad Cow's Disease"), which is caused by the mis-folding of Prion, and Alzheimer's disease, also caused by misfolded proteins.
IBM's
Blue Gene Project will attempt to ellicit the same info, except on a more detailed and granular level, using a centralized, massive multiprocessor system. Vijay Pande and his F@H group at Stanford, posit that folding sequences can be predicted just as accurately in the distributed computing model, as could be done with massive, centralized super computing, and that total, step-by-step biochemical sequencing is not necessary to show what occurs during the nanoseconds that it takes for a protein to fold.
At this point, F@H has already simulated (and I expect published) the folding of Betahairpin and villin - with some apparent additional info having been obtained regarding villin (something recently announced on the F@H newsgroup). There are a number of proteins now being analysed, so some very interesting results are sure to be forthcoming.
[EDIT: Just wanted to add that I recall Vijay mentioning an attempt to get the Betahairpin results published in Nature magazine. I didn't get chance to follow up on whether this has happened or what...]