Hi Scott,

Your questions are the right ones to be asking IMHO. Here's my answer. I'm sure the DF guys might have a different perspective and I'm not sure there is any "right" answer. Well, actually, there may be (see below).

(1) "Saying DF is able to accomplish what they hope to accomplish (in other words, giving them the benefit of the doubt and good luck), what does that really mean?"

I was trying to pull some specifics out of them on this one. Do they expect to be #1 overall in CASP? It doesn't take much to be #1 for a particular protein (and definitely not much to be #2 in a single protein -- many groups can claim that). I want DF to come out and say "we're going to be the best at CASP5, as judged by the CASP5 evalaulators, or we'll admit we were wrong and perhaps agree that the rest of the community might be right that decoy discrimination is the real problem.

(2) "How valuable to the scientific community would DF's contribution be?"

If they're #1 at CASP5 across the board with nobody else close, they'll be heros. David Baker's group did that in CASP4 and got such recognition (there's a good article in Wired Magazine about this last year). If they're in with the rest of the pack, then they'll be forgotten.

I haven't seen anything yet that makes me think they'll be able to beat all others in CASP, and note that they're not claiming they will. However, if they're not the best and they're using all this CPU time, it seems like a waste (why use 1000s of computers using DF's algorithms when Baker can do it with much less).

(3) "How does it compare against Folding@Home's value to science?" They're asking different questions, so it's a little apples & oranges. In terms of Folding@Home's comparison to its competition, it has already done what's never been done and is well recognized for that. I think if you asked the big shots in protein folding, they'd agree that Folding@Home has been able to use DC to do what's never been possible before.

Anyway, I agree DF should be given the benefit of the doubt, but for only so long. If they do poorly in CASP5 (or just average/above average), I think the honeymoon is over!

Raj