598: CASP10 Refinement Puzzle: TR712

Closed since over 13 years ago

Summary

• Created: July 10, 2012
• Expires: July 22, 2012 at 04:00 UTC
• Max points: 100

Description

This is the eleventh CASP10 Refinement Target. This model was the best server prediction for target T0712, generated by the MUFOLD-Server. We've been told that ~92% of this model matches the native! So (for once) you won't need to change the starting model much. In addition, the organizers have told us "Regions worth specific attention: 43-52, 79-92, 104-118." These are highlighted in Note Mode.

Top groups

• 1. Contenders 100 pts. 13,022
• 2. Anthropic Dreams 83 pts. 13,022
• 3. Beta Folders 68 pts. 12,958
• 4. foldeRNA 55 pts. 12,915
• 5. Void Crushers 44 pts. 12,909
• 6. HMT heritage 35 pts. 12,887
• 7. Russian team 27 pts. 12,816
• 8. L'Alliance Francophone 21 pts. 12,782
• 9. Go Science 16 pts. 12,782
• 10. Needles and Pins 12 pts. 12,715

Top soloists

• 11. smilingone 79 pts. 12,901
• 12. tokens 78 pts. 12,897
• 13. martinzblavy 76 pts. 12,883
• 14. O Seki To 74 pts. 12,877
• 15. petr2 72 pts. 12,870
• 16. grogar7 70 pts. 12,866
• 17. randomlil 69 pts. 12,865
• 18. Timo van der Laan 67 pts. 12,859
• 19. Bletchley Park 65 pts. 12,844
• 20. BitSpawn 64 pts. 12,831

Comments

[beta_helix]

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=170

Note that the organizers gave us this hint:

"Starting model GDT_TS=92. Regions worth specific attention: 43-52, 79-92, 104-118."

GDT_TS=92 essentially means that 92% 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 18, 20, 42 & 148 are highly predicted to be part of a sheet. However, the Valine at residue 105 is predicted to be in anything.