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584: Advanced CASP10 Refinement Puzzle: TR679
Status: Closed

Summary

Name: 584: Advanced CASP10 Refinement Puzzle: TR679
Status: Closed
Created: 06/25/2012
Points: 100
Expired: 07/05/2012 - 23:59
Difficulty: Advanced
Description: Not only is the eighth CASP10 Refinement Target 223 residues, but this best server prediction for target T0679 was generated by the RosettaServer (using Rosetta@home). Because of this, we are giving you the Rosetta model as a template using the Alignment Tool minus the regions the CASP assesors have told us are incorrect; start by threading it and fixing the cutpoints. This one will be tough, so we are giving you 10 days. More info in the puzzle comments.
Categories: CASP10, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 4 days 8 hours ago. Offline
Joined: 05/09/2008
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HINTS:

The CASP organizers (who have seen the native solved structure of this protein) have told us:

"Regions showing significant deviation: 25-45, 146-156, 187-197."

These are the 3 regions that you'll need to work on, after you thread the Rosetta model using the Alignment Tool.

You'll probably want to freeze the rest of the protein while you initially refine these 3 regions.

beta_helix's picture
User offline. Last seen 4 days 8 hours ago. Offline
Joined: 05/09/2008
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More info here:

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=139

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.

You'll notice that the secondary structure predictions in the regions you need to work on (residues 25-45, 146-156 & 187-197) don't tell you very much!

marie_s's picture
User offline. Last seen 1 year 28 weeks ago. Offline
Joined: 05/18/2008
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why so much conflicts ?

in the "good" parts?

brow42's picture
User offline. Last seen 7 weeks 2 days ago. Offline
Joined: 09/19/2011
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it's an extended chain

the chain 25-45 runs right down the middle of the puzzle clashing with everything. Use the cut tool to move it outside.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons