beta_helix Staff Lv 1
Here is the CASP link for this target (showing the amino acid sequence):
http://predictioncenter.org/casprol/target.cgi?id=71
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 106 & 120 are highly predicted to be part of a sheet. However, the Valine at residue 57 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=3i12
http://www.pdb.org/pdb/explore/explore.do?structureId=3gdb
http://www.pdb.org/pdb/explore/explore.do?structureId=2rct
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This target will also be posted as a trimer in the next round.
You may have noticed that the CASP organizers have told us that "The protein is known to form very stable homo-trimers."
We will post this CASP target with symmetry in the next round, when we give you the server predictions as starting models.
Symmetry doesn't currently work with the alignment tool, so there was no way to do that for this puzzle.
