Closed since over 13 years ago
Advanced Overall PredictionNot 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.
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.
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!
in the "good" parts?
the chain 25-45 runs right down the middle of the puzzle clashing with everything. Use the cut tool to move it outside.
