Fri, 12/02/2011 - 18:42
#2
Regarding the W-Y-I sequence at 26-28...
It seems like the placement and identity of the other segments force that sequence to be a loop, rather than a (as predicted by the server to be slightly more likely) sheet.
Mon, 12/05/2011 - 01:45
#3
Is this a previously unsolved
Is this a previously unsolved protein, or is this just enhancing a known or previously predicted structure?
I can't tell from the CASP site, since 90% of what's on there is gibberish to a layman.
Mon, 12/05/2011 - 05:35
#4
CASP ROLL just started last week
so these are all blind targets where the natives have not been released yet.
Here is the target list so you can see when the expiration deadlines are: http://predictioncenter.org/casprol/targetlist.cgi
![](http://128.95.1.228:8000/tracking_pixel.gif?events=scAdd&f=1111&wdata={"x":12, "y":11}){kind=tracking}
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 Valine at residue 3 is highly predicted to be part of a sheet. However, the Valine at residue 116 is predicted to be anything.