615: CASP10 Refinement Puzzle: TR754

Closed since over 13 years ago

Summary

• Created: August 07, 2012
• Expires: August 14, 2012 at 23:59 UTC
• Max points: 100

Description

This is the twenty-fourth and final CASP10 Refinement Target. This model was the best server prediction for target T0754, generated by the Zhang Server. We've been told that ~77% of this model matches the native, so you'll need to refine ~23% of the structure. Luckily, this target only has 68 residues. More info in the puzzle comments.

Top groups

• 1. Anthropic Dreams 100 pts. 9,463
• 2. Contenders 83 pts. 9,414
• 3. Beta Folders 68 pts. 9,373
• 4. foldeRNA 55 pts. 9,356
• 5. putting the eat in meat 44 pts. 9,343
• 6. Void Crushers 35 pts. 9,336
• 7. Go Science 27 pts. 9,327
• 8. L'Alliance Francophone 21 pts. 9,290
• 9. HMT heritage 16 pts. 9,284
• 10. Deleted group pts. 9,255

Top soloists

• 221. Jwagon 1 pt. 8,393
• 222. GreekCivilization 1 pt. 8,393
• 223. Hiro Protagonist 1 pt. 8,371
• 224. FlyingNinja 1 pt. 8,366
• 225. groveda 1 pt. 8,358
• 226. bull 1 pt. 8,355
• 227. fusion 1 pt. 8,354
• 228. dbjennings 1 pt. 8,347
• 229. steamywindow 1 pt. 8,338
• 230. roman madala 1 pt. 8,319

Comments

[beta_helix]

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=211

Note that the organizers gave us this hint:

"Starting model's GDT_TS=77."

GDT_TS=77 essentially means that ONLY 77% 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 58 is highly predicted to be part of a helix. However, the Valine at residue 2 is predicted to be in a sheet.