Why can't I see this in my list of puzzles?
Really want to get to work on this one...
Enjoy!
For what it's worth, the solution that has worked best for me so far, is quite along the lines of the prediction, yet also different in areas from the starting structure.
I just thought it would be good to emphasize that looking at this image helps a lot when trying to figure out where to put things. Don't just rely on the starting structure given, use the server image to look at areas you might deviate from the starting structure with. This is how mine ended up.
Not claiming that mine is right, just saying a little exploration, even within the boundaries of the prediction can yield some pretty good results.
One thing I've noticed in the high-scoring solutions I've seen for these de novo puzzles is that any sheets tend to be unnaturally straight. In real-world proteins (see the recently-completed 419 as an example) sheets are usually curved, but this is difficult to achieve in FoldIt, particularly when one starts with a perfectly straight sheet as happens in these puzzles.
A personal preference this; but I think trying to fold from a totally unfolded protein is too purist an approach. I'd rather have a few random Rosetta@home predictions to start from (you could use them to populate the Alignment tool).
@spv
I agree, I really think the sheet from 3 to 12 is pleated, and find manually pleating sheets very difficult in this software, I have not been able to do so well enough to net any gain.
I think is also why compression scripts work so well on de-novo puzzles, it allows the sheets to kind of wrap around and fill in the areas they need to get to...
I do not know about getting serve data for SS's. Any pointers and clues are appreciated.
![](http://128.95.1.228:8000/tracking_pixel.gif?events=scAdd&f=1111&wdata={"x":12, "y":11}){kind=tracking}
As requested in the feedback, http://fold.it/portal/node/989298 these secondary structure predictions have been pre-loaded into this freestyle puzzle.
Here is the sequence logo predicted by the SAM server.
H = helix
E = sheet
C = loop (or coil)
The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.
For example, the amino acid Leucine at residue 20 is highly predicted to be part of a helix. However, the Leucine at residue 16 is equally predicted to be anything.