Wed, 07/25/2012 - 19:58
#2
let's talk about the C-end
From the initial pose of this puzzle, after changing the structures to match (more or less) the predicted structures it's apparent that the high seg end (C-end) has a pose that doesn't match the predicted structures.
ADVERTISEMENT: ;-)
consider the new ScriptV2 version of my "autogen structure code V1" as an aid for saving and sharing changed structure codes, e.g. when the predicted structures differ a lot from the initial structures as they do here.
http://fold.it/portal/recipe/43480
Sun, 08/05/2012 - 05:12
#3
As pointed out here
As pointed out here (http://fold.it/portal/node/993286) the above image has disappeared!
It can be found here:
http://fold.it/portal/files/images/seqLogo_46.thumbnail.png
![](http://128.95.1.228:8000/tracking_pixel.gif?events=scAdd&f=1111&wdata={"x":12, "y":11}){kind=tracking}
Please note that the Cut Tool is available on this puzzle!
This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=190
The CASP10 organizers gave us this hint:
"Starting model GDT_TS=86."
GDT_TS=86 essentially means that 86% of the model superimposes correctly onto the native structure:
http://en.wikipedia.org/wiki/Global_distance_test
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 Valines at residues 48, 140 & 168 are highly predicted to be part of a helix. However, the Valines at residues 68, 99, 127 & 153 are predicted to be part of a sheet.