612: Quick CASP10 Refinement Puzzle: TR722

Closed since over 13 years ago

Summary

• Created: August 02, 2012
• Expires: August 09, 2012 at 17:00 UTC
• Max points: 100

Description

As mentioned in Puzzle 608: this Rosetta model was the best server prediction for target T0722, but only ~58% of this model matches the solved structure. We are giving you this model without symmetry, in case it folds up as a monomer. This quick puzzle is worth 70 global points. More info in the puzzle comments.

Top groups

• 1. Anthropic Dreams 100 pts. 11,040
• 2. Void Crushers 77 pts. 11,024
• 3. Contenders 58 pts. 11,024
• 4. Beta Folders 43 pts. 10,942
• 5. Russian team 31 pts. 10,920
• 6. L'Alliance Francophone 22 pts. 10,846
• 7. Go Science 15 pts. 10,834
• 8. SETI.Germany 11 pts. 10,831
• 9. Deleted group pts. 10,821
• 10. foldeRNA 5 pts. 10,802

Top soloists

• 161. mbinfield 1 pt. 9,990
• 162. jo8i1 1 pt. 9,888
• 163. barbaranne 1 pt. 9,450
• 164. Neroje 1 pt. 9,450
• 165. Simek 1 pt. 9,450
• 166. steveB 1 pt. 9,450
• 167. Wildcat777 1 pt. 9,450
• 168. Vie 1 pt. 9,450

Comments

[beta_helix]

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=195

Note that the organizers gave us this hint:

"Starting model GDT_TS=58."

GDT_TS=58 essentially means that ONLY 58% 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 Valines at residues 23, 55, 85, 94, 112 & 115 are highly predicted to be part of a helix. However, the Valine at residue 34 is not predicted to be anything.