Fri, 06/22/2012 - 20:35
#552
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 10, 12 & 45 are highly predicted to be part of a helix. However, the Valine at residue 93 is predicted to be in a sheet.




This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=131&view=refinement
Note that the organizers gave us this hint:
"Starting model GDT_TS=84."
GDT_TS=84 essentially means that 84% of the model superimposes correctly onto the native structure:
http://en.wikipedia.org/wiki/Global_distance_test
Secondary Structure Predictions below: