Since this is a big and nasty CASP target, we're giving you just one server model to work on this time... hopefully this helps reduce the crashes with this target.
Here is a link to the previous round of this puzzle, with SS predictions and more:
This has a section that is either bad, or its a binding site; not sure which. On such a large protein, is it useful to make major changes that I know will score better, but i have no real expectation that it is more accurate, or should I stick with the general arrangement and make modifications where I see potential problems?
Great question, karstenw!
The CASP organizers had already posted this one as a CASP ROLL target last year:
(Maybe it looked a bit familiar: https://fold.it/portal/node/996451 :-)
but I think it’s such an interesting one that they wanted the human CASP11 groups to take a stab at it.
They already told us that it’s a dimer (which they hadn’t mentioned in CASP ROLL) and check out the trans-membrane prediction:
Because of all of this, our confidence in this server model is quite low, so you should feel free to try very drastic topological changes (rather than just trying to find the top-scoring conformation closest to the starting structure).
So even if we create a solution with a different topology when we know the native is a dimer, we have little chance of making it score in CASP or foldit unless we get the other part, assuming you can work out what the sym is?
I'm not entirely sure what you're getting at, but maybe this will help:
Some of the targets in CASP are known to self-associate (form dimers, trimers, etc.), and CASP provides this information so that it might help you predict the structure of the monomer. However, it is not necessary to predict the structure of the full multimer. For example, for target T0763, CASP assessors will compare your monomer prediction with a single subunit of the dimer. Some groups may also submit predictions for the full dimer, but those predictions will be evaluated separately.
If we knew the symmetry of the dimer, we would run this target as a symmetry puzzle.
hopefully it is not like 3ks7 which would be a lovely sym puzzle :D
In CASP10 we were fortunate to correctly guess the symmetry of one of the refinement targets (TR722), so we were able to post it as a symmetry puzzle: http://fold.it/portal/node/993251#comment-19148
It was this target that our WeFold collaborators were able to pick out and improve one of your Foldit predictions, resulting in the best CASP submission for that target (wfFUIK): http://fold.it/portal/files/Slide2.png
So, if for any CASP11 targets you are find some evidence of symmetry, please do let us know!
But I don't know if everyone would agree that a 397 symmetry puzzle would be lovely :-P
My eyes... they burn....