(1) plaidfishes: Interesting post. It's clear that you've though about this, but I guess I disagree with you in several areas, but perhaps it's just me.

First, protein structure prediction is not really considered to be a computer science problem and neither is distributed computing. Protein structure prediction is a problem is molecular biology and distributed computing involves no new CS. The interesting aspects have to come from their relevance to biology. Oh, and there are nobel prizes awarded to biologists (medicine and physiology), but not that that matters. I brought that up to stress the importance of the problem.

Second, are you familiar with DF's peers? To claim they are head and shoulders above them, you need to be able to make a true comparison. Are you familiar with how DF did in CASP relative to their peers? If you did, I think you might want to retract your statement. Perhaps distirbuted computing will make the difference. Let's see how CASP5 turns out. From my posts, it's clear I'm willing to be that CASP5 might not be the DF-fest that one would like.

So, in summary, I'm not sure that the average DC user is capable to judge the science going on here. One needs to look to how the scientific community views it. That's again why I mention CASP. If DF can't get the community excited about their work, it's probably not that great. It's too early to tell right now. We'll know by the end of the year when the CASP5 results are announced.


(2) "protein folding is NP complete" This is an interesting question. Certainly, blindly testing all the possibilities is NP complete. However, somehow Nature seems to solve the problem easily. From experiments, it's clear that Nature *does not* look through all of the possibilities and thus Nature's algorithm appears to not be NP complete. Indeed, the folding rate of proteins largely appears to be independent of length (see a recent JMB by Plaxco, Simmons, and Baker).

Thus, Nature's dynamics of folding evades this issue. This is another reason why Nature's method is interesting (to me, and many in the field) and on reason why Blue Gene and FAH are looking to understand it. (again, this is not to say that BG and FAH are trying to do structure prediction!!! but rather to understand how Nature does it)

(3) Shaktai. Good point that "no well meaning effort is wasted" BUT, we do have a limited amount of resources in the world, and one should be judicious with its allocation. Again, I should stress that DF deserves it's chance (even if there are naysayers that say it won't work). Just if it's shown not to work (or at least not to be as good as other methods, eg Baker's), it's time to move on and give someone else a chance (and allowing their well meaning effort not to be wasted).

(4) I look back at my own posts and many aspects seem to have a negative tone. Sorry about that, it's not really fair or appropriate. I'm trying to just bring up the important isues, which I feel have been skirted. As I've said before, let's hope that DF kicks ass in CASP and then we'll have the validation necessary!

Raj