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583: Large CASP10 Refinement Puzzle: TR689
Status: Closed
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Summary
| Name: |
583: Large CASP10 Refinement Puzzle: TR689 |
| Status: |
Closed |
| Created: |
06/23/2012 |
| Points: |
100 |
| Difficulty: |
Intermediate |
| Description: |
The seventh CASP10 Refinement Target has 234 residues! This model was the best server prediction for target T0689, generated by the Jiang_Fold server. We've been told that ~87% of this model matches the native, so you just need to find which 13% to refine! We are giving you a couple extra days to work on this one due to its size. More info in the puzzle comments. |
| Categories: | CASP, Overall, Prediction |
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![](http://128.95.1.228:8000/tracking_pixel.gif?events=scAdd&f=1111&wdata={"x":12, "y":11}){kind=tracking}
This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=132
Note that the organizers gave us this hint:
"Starting model GDT_TS=87."
GDT_TS=87 essentially means that 87% of the model superimposes correctly onto the native structure:
http://en.wikipedia.org/wiki/Global_distance_test
We believe that Jiang_Fold_TS1.pdb is identical to the refinement model.
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 34, 49, 54, 57, 66, 71 & 183 are highly predicted to be in sheets. However, the Valines at residues 3, 107, 137 & 144 are predicted to be anything.