614: CASP10 Refinement Puzzle: TR724

Closed since over 13 years ago

Summary

• Created: August 03, 2012
• Expires: August 13, 2012 at 22:00 UTC
• Max points: 100

Description

The twenty-third CASP10 Refinement Target was the best server prediction for target T0724, generated by the slbio server. We've been told that ~60% of this model matches the native, so you'll need to significantly change the starting model. More info in the puzzle comments.

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• 40. Alistair69 39 pts. 10,580

Comments

[beta_helix]

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=209

The CASP10 organizers gave us this hint:

"Starting model GDT_TS=60."

GDT_TS=60 essentially means that 60% 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 35, 44, 53, 63 & 87 are highly predicted to be part of a sheet. However, the Alanines at residues 11 & 49-50 are predicted to be in anything.