607: Beginner CASP10 Refinement Puzzle: TR747

Closed since over 13 years ago

Summary

• Created: July 27, 2012
• Expires: August 04, 2012 at 13:00 UTC
• Max points: 100

Description

This is the seventeenth CASP10 Refinement Target. This model was the best server prediction for target T0747, generated by the Mufold server. We've been told that ~83% of this model matches the native, so you just need to find which 17% to refine! Luckily, this is a short target with only 98 residues. More info in the puzzle comments.

Top groups

• 1. Anthropic Dreams 100 pts. 10,637
• 2. Contenders 81 pts. 10,634
• 3. Beta Folders 65 pts. 10,604
• 4. foldeRNA 52 pts. 10,593
• 5. HMT heritage 41 pts. 10,543
• 6. Go Science 32 pts. 10,543
• 7. L'Alliance Francophone 24 pts. 10,543
• 8. FoldIt@Netherlands 18 pts. 10,533
• 9. Void Crushers 14 pts. 10,530
• 10. Gargleblasters 10 pts. 10,494

Top soloists

• 1. gitwut 100 pts. 10,634
• 2. BitSpawn 98 pts. 10,633
• 3. gmn 96 pts. 10,630
• 4. doug.ehlert 94 pts. 10,624
• 5. smilingone 92 pts. 10,604
• 6. stg123123 90 pts. 10,594
• 7. Deleted player pts. 10,593
• 8. johnmitch 86 pts. 10,585
• 9. jamiexq 84 pts. 10,580
• 10. bertro 82 pts. 10,566

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=204

Note that the organizers gave us this hint:

"Starting model GDT_TS=83."

GDT_TS=83 essentially means that ONLY 83% 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 24, 46, 48, 90 & 92-93 are highly predicted to be part of a sheet. However, the Valine at residue 11 is predicted to be anything.