beta_helix's picture
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Joined: 05/09/2008
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Additional info about this CASP target

Here is the CASP link for this target (showing the amino acid sequence):
http://predictioncenter.org/casp10/target.cgi?id=70
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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 6, 7, & 10 are highly predicted to be in a helix. However, the Valines at residues 59, 60, 64 & 65 are predicted to be in a sheet.
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Link to template PDBs:

http://www.pdb.org/pdb/explore/explore.do?structureId=3s4k
http://www.pdb.org/pdb/explore/explore.do?structureId=1olp
http://www.pdb.org/pdb/explore/explore.do?structureId=2w9q
http://www.pdb.org/pdb/explore/explore.do?structureId=2e12
http://www.pdb.org/pdb/explore/explore.do?structureId=3e1e
http://www.pdb.org/pdb/explore/explore.do?structureId=1q6w

Keep in mind that it's very likely that ONLY ONE of these templates is close to the native (if we're lucky!)

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