586: Large CASP10 Refinement Puzzle: TR681

Closed since over 13 years ago

Summary

• Created: June 25, 2012
• Expires: July 05, 2012 at 10:00 UTC
• Max points: 100

Description

The eighth CASP10 Refinement Target has 224 residues! This model was the best server prediction for target T0681, generated by the MULTICOM-CONSTRUCT server. We've been told that ~78% of this model matches the native, so you just need to find which 22% to refine! We are giving you a couple extra days to work on this one due to its size. More info in the puzzle comments.

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• 80. WBarme1234 15 pts. 12,620

Comments

[beta_helix]

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=140

Note that the organizers gave us this hint:

"Starting model GDT_TS=78."

GDT_TS=78 essentially means that 78% 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 MULTICOM-CONSTRUCT_TS3.pdb is identical to the refinement model.

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 Leucines at residues 14-15 are highly predicted to be in a helix. However, the Leucines at residues 54 & 86 are predicted to be part of a sheet.