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573b: Advanced CASP10 Refinement Puzzle: TR663
Status: Closed

Summary

Name: 573b: Advanced CASP10 Refinement Puzzle: TR663
Status: Closed
Created: 06/11/2012
Points: 100
Expired: 06/16/2012 - 23:59
Difficulty: Advanced
Description: The CASP organizers have told us that two regions of this starting model are incorrect, so we have modified both these regions into 2 extended chains. You can use the alignment tool to thread the remaining original regions. We will repost this puzzle using the unmodifided starting model, letting you load in your solutions from this puzzle. Secondary structure predictions for this Refinement target are posted in the puzzle comments.
Categories: CASP10, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 1 hour 51 min ago. Offline
Joined: 05/09/2008
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Additional info about this CASP10 Refinement target

Here is the CASP link for this Refinement target:
http://predictioncenter.org/casp10/target.cgi?id=103&view=refinement
____________________________________________________

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 32 & 115 are highly predicted to be in a sheet. However, the Leucine at residue 103 is predicted to be in a helix.

beta_helix's picture
User offline. Last seen 1 hour 51 min ago. Offline
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As requested in this comment:

http://fold.it/portal/node/992917#comment-18188
we have reposted this puzzle with the alignment tool so that you can now use the cut tool.

Additionally, if you thread the template it will give you the exact starting model minus the regions they told us to fix.

Those regions can also be viewed in Note Mode.

You can load in your solutions from the previous version of this puzzle (http://fold.it/portal/node/992917) by making manual saves.

brow42's picture
User offline. Last seen 3 days 6 hours ago. Offline
Joined: 09/19/2011
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Secondary Structure

The logo seems to have disappeared but Datacute found it for me (perhapse he used the Google search box?) Here it is:

Also I reran the SAM 08 myself, here's what I got (paste this into AA Copy Paste Compare):

H 4-5 H 13-23 E 29-36 E 41-48 E 53-59 E 65-66 H 70-72 H 75-78 H 82-86 H 89 H 95-105 E 110-116 E 121-129 E 134-140 E 146-151

brow42's picture
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beta_helix's picture
User offline. Last seen 1 hour 51 min ago. Offline
Joined: 05/09/2008
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Thanks brow42, I don't know where it went!

It has been reposted in the original comment above as well.

UPDATE, it keeps vanishing, I'll try to post it here:

marie_s's picture
User offline. Last seen 1 year 20 weeks ago. Offline
Joined: 05/18/2008
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the comments are annoying on the screen

Please put comments in these comments not on the puzzle.

Dont forget, foldit works because it is a game, not a work, not a tool to learn things, not a mean to select students...

So you can give advices, why not, but the spirit of foldit is exploring without previous knowledges.

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