604: CASP10 Refinement Puzzle: TR698

Closed since over 13 years ago

Summary

• Created: July 22, 2012
• Expires: August 02, 2012 at 06:00 UTC
• Max points: 100

Description

This is the fourteenth CASP10 Refinement Target. This model was the best server prediction for target T0698, generated by the PMS server. We've been told that ~65% of this model matches the native, so you'll need to significantly change the starting model. Luckily, they have told us which regions require special attention: residues 17-35 & 90-100. These regions are shown in Note Mode. More info in the puzzle comments.

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Comments

[beta_helix]

Please note that the Cut Tool is available on this puzzle!

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=188

The CASP10 organizers gave us this hint:

"Starting model GDT_TS=65. Regions 17-35 and 90-100 need special attention."

GDT_TS=65 essentially means that 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 23-25 & 104 are highly predicted to be part of a helix. However, the Valines at residues 91 & 95 are predicted to be in anything.