Hi,
Seems like this thread is nearing its end in terms of productive discussion. It will be interesting to see how the protein strucutre prediction field progresses. Perhaps it makes sense to revisit these questions at the end of the year. It's interesting that Dr. Hogue called these posts "FUD". I guess we'll see for sure post CASP.
Raj
PS As to Dr. Hogue's points.
(1) molecular dynamics is usually O(N), eg with cuttoffs of Particle-Mesh Ewald
(2) I found your point very interesting about the quote on the FAH paper, so I took a look. At first sight, I thought you raised a very serious point. After some reading and some thinking, I think you might be missing the point with the potentials used in MD. These potentials don't make good discriminators for structure prediction (as stated in the FAH paper), but that doesn't mean they don't make good force fields for MD. Remember that potentials used in MD are energies, not complete free energies and thus there are conformational entropies (side chains, minor backbone variations, etc) which are also relevant. These entropies come automatically in MD (which samples with Boltzmann weighting). Thus, the force fields won't necessarily be able to discrimiante or act as scoring functions for structure prediction, but may be perfectly fine for MD and kinetics. I think the FAH result shows that they're pretty good for folding kinetics (although probably far from perfect). Anyway, you should probably ask the FAH people. They might have a better (or at least different) answer.