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613: CASP10 Refinement Puzzle: TR655
Status: Closed

Summary

Name: 613: CASP10 Refinement Puzzle: TR655
Status: Closed
Created: 08/03/2012
Points: 100
Expired: 08/12/2012 - 20:00
Difficulty: Advanced
Description: The twenty-second CASP10 Refinement Target was the best server prediction for target T0655, generated by the Tasser_VMT server. We've been told that ~69% of this model matches the native, so you'll need to significantly change the starting model. Luckily, they have told us which regions to focus on 1-15 & 46-59 (as well as which to ignore: residues 86-88 & 137-158). These regions are shown in Note Mode. More info in the puzzle comments.
Categories: CASP10, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 3 days 16 hours ago. Offline
Joined: 05/09/2008
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More info here:

Please look at the Notes for this puzzle (by pressing 3 in the Original Interface, or pressing 1 in the Selection Interface).

************

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=212

The CASP10 organizers gave us this hint:

"The experimental NMR structure shows quite a bit of disorder in regions 91-93 and 142-163. Regions 6-20 and 51-64 need special attention. Starting model GDT_TS=69 (including the internal disordered regions)."

GDT_TS=69 essentially means that 69% of the model superimposes correctly onto the native structure:
http://en.wikipedia.org/wiki/Global_distance_test

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 Valine at residue 92 is highly predicted to be part of a sheet. However, the Valine at residue 92 is predicted to be in a helix.

Joined: 05/19/2009
Groups: Contenders
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brow42's picture
User offline. Last seen 8 weeks 1 day ago. Offline
Joined: 09/19/2011
Groups: None
It's there now 8:00 PDT 15:00

It's there now 8:00 PDT 15:00 GMT.

Susume's picture
User offline. Last seen 6 hours 57 min ago. Offline
Joined: 10/02/2011
"Disorder" is not clear to me

"Disorder" is not clear to me - does that mean those areas will not be scored for CASP so it doesn't matter if we move them?

beta_helix's picture
User offline. Last seen 3 days 16 hours ago. Offline
Joined: 05/09/2008
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They haven't been very clear on this.

Normally, disordered regions will not be scored.
See TR754 as an example:
http://predictioncenter.org/casp10/target.cgi?id=211&view=refinement
"Residues 1-8 and 77-80 are disordered in the experimental structure and deleted from the model."

It probably means that they will simply ignore that region (but you never know... they have never mentioned this sort of thing in previous CASPs), I would just not worry about those regions and focus on Regions 6-20 and 51-64.

Sequence Logo can be found here (since it keeps vanishing):
http://fold.it/portal/files/images/seqLogo_52.png

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