609: Beginner CASP10 Refinement Puzzle: TR696

Closed since over 13 years ago

Summary

• Created: July 30, 2012
• Expires: August 08, 2012 at 12:00 UTC
• Max points: 100

Description

This is the nineteenth CASP10 Refinement Target. This model was the best server prediction for target T0696, generated by the Bilab-Enable server. We've been told that ~71% of this model matches the native, so you just need to find which 29% to refine! Luckily, this is a short target with only 100 residues. More info in the puzzle comments.

Top groups

• 1. Beta Folders 100 pts. 10,464
• 2. Contenders 81 pts. 10,459
• 3. Anthropic Dreams 64 pts. 10,373
• 4. L'Alliance Francophone 50 pts. 10,353
• 5. Void Crushers 39 pts. 10,339
• 6. Go Science 30 pts. 10,291
• 7. Deleted group pts. 10,235
• 8. Russian team 17 pts. 10,220
• 9. foldeRNA 12 pts. 10,218
• 10. HMT heritage 9 pts. 10,118

Top soloists

• 111. Bautho 4 pts. 9,812
• 112. jogie62 4 pts. 9,802
• 113. silverberg 4 pts. 9,793
• 114. truestone 3 pts. 9,790
• 115. tscherulli 3 pts. 9,786
• 116. Brewster 3 pts. 9,762
• 117. sbea3 3 pts. 9,724
• 118. histon 3 pts. 9,704
• 119. lamoille 3 pts. 9,701
• 120. Chris67 3 pts. 9,696

Comments

[beta_helix]

NOTE: The Cut Tool IS available for this puzzle, but only in the Developer Preview.
(If you want to try it out, please read "How do I try out the Foldit Developer Preview?" in the FAQ: http://fold.it/portal/info/faq )
Once the next update posts (early next week) the Cut Tool will be available in main.
__________________

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=196

Note that the organizers gave us this hint:

"Starting model GDT_TS=71."

GDT_TS=71 essentially means that ONLY 71% of the model superimposes correctly onto the native structure:

en.wikipedia.org

Global distance test

The global distance test (GDT), also written as GDT_TS to represent "total score", is a measure of similarity between two protein structures with known amino acid correspondences (e.g. identical amino acid sequences) but different tertiary structures. It is most commonly used to compare the results of protein structure prediction to the experimentally determined structure as measured by X-ray crystallography, protein NMR, or, increasingly, cryoelectron microscopy. The metric was developed by Ada...

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 19 is highly predicted to be part of a helix. However, the Valine at residue 92 is highly predicted to be in a sheet.