603: CASP10 Refinement Puzzle: TR705

Closed since over 13 years ago

Summary

• Created: July 22, 2012
• Expires: July 31, 2012 at 16:00 UTC
• Max points: 100

Description

This is the thirteenth CASP10 Refinement Target. This model was the best server prediction for target T0705, generated by the AOBA-server. We've been told that ~65% of this model matches the native, so you'll need to significantly change the starting model. Luckily, this is a short target with only 96 residues. Note: Cut Tool is available on this puzzle.

Top groups

• 11. Russian team 7 pts. 10,078
• 12. Gargleblasters 5 pts. 10,012
• 13. SETI.Germany 4 pts. 9,894
• 14. Natural Abilities 3 pts. 9,821
• 15. Deleted group pts. 9,797
• 16. Richard Dawkins Foundation 1 pt. 9,729
• 17. 7Monkeys 1 pt. 9,698
• 18. Czech National Team 1 pt. 9,612
• 19. Team Canada 1 pt. 9,439
• 20. Team China 1 pt. 9,351

Top soloists

• 51. Rav3n_pl 29 pts. 10,136
• 52. Bletchley Park 28 pts. 10,133
• 53. djag 27 pts. 10,129
• 54. Flagg65a 27 pts. 10,124
• 55. harvardman 26 pts. 10,122
• 56. randomlil 25 pts. 10,120
• 57. Ribo-soma 24 pts. 10,114
• 58. pgiles 24 pts. 10,108
• 59. jamiexq 23 pts. 10,108
• 60. brow42 22 pts. 10,107

Comments

[beta_helix]

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=192

Note that the organizers gave us this hint:

"Starting model GDT_TS=65."

GDT_TS=65 essentially means that ONLY 65% 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 19, 20 & 76 are highly predicted to be part of a sheet. However, the Valine at residue 38 is predicted to be anything.