beta_helix Staff Lv 1
Here is the CASP link for this target (showing the amino acid sequence):
http://predictioncenter.org/casproll/target.cgi?id=69
You'll notice that the sequence we have given you has been trimmed (compared to the one on the CASP ROLL website). This is because the N-terminus is predicted to be a signal peptide by the Rosetta Server:
http://rosettaserver.bakerlab.org/results.jsp?id=34809
For more info on that: http://en.wikipedia.org/wiki/Signal_peptide
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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 104 is highly predicted to be part of a loop. However, the Valine at residue 47 is not predicted to be anything!
The above predictions are already on the starting model (based on the horizontal lines in the above figure).
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Link to template PDBs:
http://www.pdb.org/pdb/explore/explore.do?structureId=1sr3 http://www.pdb.org/pdb/explore/explore.do?structureId=4ex5 http://www.pdb.org/pdb/explore/explore.do?structureId=1qzg
