579: Beginner CASP10 Refinement Puzzle: TR662

Closed since over 13 years ago

Summary

• Created: June 15, 2012
• Expires: June 24, 2012 at 12:00 UTC
• Max points: 100

Description

This is the fourth CASP10 Refinement Target. This model was the best server prediction for target T0662, generated by the Zhang server. We've been told that ~84% of this model matches the native, so you just need to find which 16% to refine! More info in the puzzle comments.

Top groups

• 21. Nerdfighters 1 pt. 9,567
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• 24. Geekdo 1 pt. 8,368

Top soloists

• 1. enszyme 100 pts. 9,918
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• 6. Bletchley Park 91 pts. 9,897
• 7. mimi 89 pts. 9,896
• 8. jtollenaar 87 pts. 9,894
• 9. O Seki To 86 pts. 9,894
• 10. utaca 84 pts. 9,892

Comments

[beta_helix]

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=110&view=refinement

Note that the organizers give us this as a hint:

"N-term res. 1-4 are disordered in the native structure and removed from the starting model. Starting GDT_TS=84."

So, the first 4 residues have been deleted.

GDT_TS=84 essentially means that 84% 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...

We believe that Zhang-Server_TS4.pdb is identical to the refinement model (except that it obviously doesn't have the first 4 residues trimmed!)

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 8, 11, 35-36, 62 & 69 are highly predicted to be part of a helix. However, the Valines at residues 49 & 52 are predicted to be in either loops or sheets.