591: Beginner CASP10 Refinement Puzzle: TR671

Closed since almost 14 years ago

Summary

• Created: July 04, 2012
• Expires: July 12, 2012 at 07:00 UTC
• Max points: 100

Description

This is the tenth CASP10 Refinement Target. This model was the best server prediction for target T0671, generated by the MUFOLD-Server. We've been told that only ~55% of this model matches the native, so (unlike previous CASP10 refinement puzzles) you'll need to significantly change the starting model. Luckily, this is a short target with only 88 residues. More info in the puzzle comments.

Top groups

• 11. Russian team 11 pts. 9,816
• 12. Richard Dawkins Foundation 9 pts. 9,780
• 13. Natural Abilities 7 pts. 9,731
• 14. Deleted group pts. 9,712
• 15. Gargleblasters 4 pts. 9,660
• 16. Deleted group pts. 9,568
• 17. SETI.Germany 2 pts. 9,550
• 18. Mojo Risin' 1 pt. 9,528
• 19. Nerdfighters 1 pt. 9,518
• 20. TT-group 1 pt. 9,412

Top soloists

• 91. djag 16 pts. 9,737
• 92. Mr_Jolty 16 pts. 9,731
• 93. petr2 16 pts. 9,727
• 94. pfeiffelfloyd 15 pts. 9,725
• 95. Mark- 15 pts. 9,720
• 96. caglar 15 pts. 9,716
• 97. SimplySue 14 pts. 9,714
• 98. Psych0Active 14 pts. 9,712
• 99. glaciall 14 pts. 9,711
• 100. Brewster 13 pts. 9,707

Comments

[beta_helix]

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=152

Note that the organizers gave us this hint:

"Starting model GDT_TS=55."

GDT_TS=55 essentially means that ONLY 55% 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...

Secondary Structure Predictions below:

[beta_helix]

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 40, 52, 73 & 86 are highly predicted to be part of a sheet. However, the Valine at residue 9 is predicted to be in anything.