Originally posted by Scott Jensen
Aegion,

In reading Raj's posts over again, I see his statements as being rather nice challenges. Challenging assumptions and reasons. Very politely worded and knowledgeable challenges at that. To say nothing about being nice enough to answer my questions and helping me understand what's Howard and him were talking about.

As for the comparison between DF and Folding@Home, I'm not quite getting you. Am I correct that what you're saying is both are going to help science to the same end but "simply" DF will be doing it in a quicker (less computationally intense) way than Folding@Home?

Also, if I'm getting you right, DF is guessing at protein structure whereas Folding@Home is not. How do you know if that guess is right? Isn't accepting anything but the exact protein a bit wrong?

For all Folding@Home's faults (and I could list plenty), one of the main reasons that attracted me to them was that they were trying to beat IBM's Blue Gene at it's own game before it even got into the ring and the results would be made free to scientists as opposed to owned by corporations. Is DF also taking on Blue Gene? Personally, I like helping the Davids of the world take on the Goliaths.
Folding@Home can also be applied in a couple other ways other than simply using the outcome of the protein fold as the information. Basicly you don't need to determine the exact shape of a folded protein absolutely perfectly for pharmaceutical companies to sucessfully use the information to devise new medicines, and this is why the Distributed Folding Project is using its current approach. A major purpose of the current phase of the project is to demonstrate that the software the project is currently using can accurately predict how far off from the true protein structure a protein actually is. If we can determine that the software is capable of predicting this accurately, we can be confident of our results when we enter the next phase of the project in which we deal with predicting the structures of proteins which we do not have complete knowledge of its shape. IBM's Blue Gene is using a less innovative method of determining the shape of a folded protein, but The Distributed Folding Project offers the possibility for people with access to smaller amounts of computing resources to also be able to determine the shape of a substancial numbers of folded proteins.