This is the best we can do?!

[Scott Jensen]

One second please.

*Scott puts on his flame-proof fireman's outfit ... including independent oxygen supply.*

Thanks for waiting.

Well, I just looked at the graphics for all the proteins we've done so far and thought to myself:

OH MY GOD, WE DID THAT BADLY?!

From what the scientists have been saying here and what I've read elsewhere, the shape of the protein determines its function and our aim is to make our simulation as close as possible to the real thing so it will do what the real one does. Too far off and the simulation is worthless ... or worse if medical drugs are developed thinking the simulation is the true structure but the simulation is so far off that the drug they're developing will have little or even bad effects on the actual real protein. And at the protein level, even an angstrom (a tenth of a billionth of a meter) difference supposedly really does matter!

When looking at the graphics of the protein structures we've already attempted to predict, I get the impression of a drunk trying to walk a drawn curvy line. Sorry, but those graphics rather depressed me as for what we're trying to accomplish here. And this is with a KNOWN protein. One where we know the RMSD score. Now we're about to do unknown ones for CASP and I cannot even imagine how far off the comparison graphic will be when we finish theirs.

As for what I was expecting, I was expecting just a slight drawing outside of the lines. Like there being a third color of green when segments exactly matched the protein with blue and yellow coming into play when they didn't ... and that would be only a few tiny times. Now if that really did happen, I'd HIGHLY recommend adding this new color and the reason for the color. Perhaps even more of a rainbow separation thing where it's green if they perfectly match and shift more to the different ends of the color spectrum the further they get apart (deep red for native and deep purple for software generated).

OK, now I'm fully expecting "love it or leave it", "it's better than nothing", and "Gosh, Scott, would you like a billion dollars?" replies to this post. Note the flame suit. However, while I expect and won't get really upset by those replies (well, especially not the last one ), I would appreciate some good scientific assurance (in layman terms) that we're not wasting our computers on this project. And did FAH do any of these proteins? If so, could you show how their graphics looked ... even a comparison graphic with DF's simulation in one color, FAH's in another color, and the real protein in a third? Perhaps real protein in green, DF in yellow, and FAH in blue.