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=65
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=34143
For more info on that: http://en.wikipedia.org/wiki/Signal_peptide
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The SAM server had problems due to a power outage, but here is a close sequence logo (just missing the first 3 residues):
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 Valines at residues 75, 89 & 92 are highly predicted to be part of a sheet. However, the Valine at residue 9 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=1qhq http://www.pdb.org/pdb/explore/explore.do?structureId=2qnk http://www.pdb.org/pdb/explore/explore.do?structureId=1avw