601: CASP10 Refinement Puzzle: TR723

Closed since over 13 years ago

Summary

• Created: July 15, 2012
• Expires: July 28, 2012 at 23:00 UTC
• Max points: 100

Description

This is the twelfth CASP10 Refinement Target. This model was the best server prediction for target T0723, generated by the Matrix server. We've been told that ~85% of this model matches the native, so you just need to find which 15% to refine! More info in the puzzle comments.

Top groups

• 11. Gargleblasters 13 pts. 10,960
• 12. Russian team 10 pts. 10,958
• 13. Deleted group pts. 10,937
• 14. Atlanta 6 pts. 10,848
• 15. Richard Dawkins Foundation 4 pts. 10,816
• 16. Deleted group pts. 10,799
• 17. Nerdfighters 2 pts. 10,792
• 18. SETI.Germany 2 pts. 10,779
• 19. Mojo Risin' 1 pt. 10,766
• 20. BOINC@Poland 1 pt. 10,740

Top soloists

• 231. groveda 1 pt. 10,370
• 232. Lebanon Expert 1 pt. 10,369
• 233. AbplanalpJ 1 pt. 10,365
• 234. Artiem 1 pt. 10,365
• 235. roman madala 1 pt. 10,364
• 236. armadillo314 1 pt. 10,364
• 237. LNZ 1 pt. 10,363
• 238. hada 1 pt. 10,358
• 239. madasian772 1 pt. 10,355
• 240. grunge28 1 pt. 10,355

Comments

[beta_helix]

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=173

Note that the organizers gave us this hint:

"Starting model GDT_TS=85."

GDT_TS=85 essentially means that 85% 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 42, 67, 86, 99, 103 & 122 are highly predicted to be part of a helix. However, the Valines at residues 17 & 94 are predicted to be anything.