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584: Advanced CASP10 Refinement Puzzle: TR679

Closed since over 13 years ago

Advanced Overall Prediction

Summary

Created
June 25, 2012
Expires
Max points
100
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.

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Comments

beta_helix Staff Lv 1

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 Staff Lv 1

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!

brow42 Lv 1

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