What is our phase now?

[matitaccia]

Yes, I feel a bit lost.

In which phase of the project are we?

I think it should be a bit more clearly said where we are and where we are going to.

The name of this protein is?
It is important for?
Expectations?

Thanks.
matitaccia

[brage]

Yes, it would be nice to know the answer to those questions. Unfortunately the admins never bother to tell us anything other than when a protein change has taken place...

This is the chaos-phase

[Galuvian]

The backend is obviously being worked on right now. . .

Although Howard and Elena have alluded to these things in the past, an actual page telling us where they are would be nice.

Here is the impression I have:

Scientifically they are working on the scoring algorithm, how to determine the lowest RMSD without using the known structure. Essentially how to find the needle in the haystack. They currently believe that the lowest energy leads to the lowest RMSD (this could be a proven fact, I don't remember).

If they can establish that link it will basically prove they are on the right track. After that they can refine the crunching algorithm to find the lowest energy score and produce the most accurate results. It doesn't make sense to spend time refining this until they have a useful scoring algorithm.

The actual proteins we are crunching aren't important. They are selecting a variety of known proteins with differing properties to allow them to test the software under as many different conditions as possible. It might satisfy some curiosity about what we are crunching but doesn't have much bearing on the project as a whole.

[tpdooley]

The proteins we've been folding in Phase II have all been ones we've worked with before. This allows them to see how much better or worse the current scoring algorithm is working compared to the pure random approach we started off with.

[Brian the Fist]

http://www.blueprint.org/proteinfold...tml#phaseiifaq

The above link may answer a few of your questions. We are presently doing one of the CASP5 targets that we did in Phase I to, as mentioned above, compare the present methods results with Phase I.