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603: CASP10 Refinement Puzzle: TR705
Status: Closed

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beta_helix's picture
User offline. Last seen 22 hours 45 min ago. Offline
Joined: 05/09/2008
Groups: None
More info here:

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=192

Note that the organizers gave us this hint:

"Starting model GDT_TS=65."

GDT_TS=65 essentially means that ONLY 65% 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 19, 20 & 76 are highly predicted to be part of a sheet. However, the Valine at residue 38 is predicted to be anything.

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