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=63
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=34040
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 Valines at residues 16, 54 & 110 are highly predicted to be part of a sheet. However, the Valine at residue 89 is predicted to be in a loop!
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=3iuu
http://www.pdb.org/pdb/explore/explore.do?structureId=2jvf
http://www.pdb.org/pdb/explore/explore.do?structureId=1qys