Tue, 05/15/2012 - 22:08
#2
Link to template PDBs:
http://www.pdb.org/pdb/explore/explore.do?structureId=1kaf
http://www.pdb.org/pdb/explore/explore.do?structureId=2p0g
http://www.pdb.org/pdb/explore/explore.do?structureId=3gfk
http://www.pdb.org/pdb/explore/explore.do?structureId=3kha
http://www.pdb.org/pdb/explore/explore.do?structureId=3ovk
http://www.pdb.org/pdb/explore/explore.do?structureId=3ui3
Keep in mind that it's very likely that ONLY ONE of these templates is close to the native (if we're lucky!)
![](http://128.95.1.228:8000/tracking_pixel.gif?events=scAdd&f=1111&wdata={"x":12, "y":11}){kind=tracking}
Here is the CASP link for this target (which has the amino acid sequence):
http://predictioncenter.org/casp10/target.cgi?id=65
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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 51 is highly predicted to be in a sheet. However, the Valine at residue 10 is not predicted to be anything.