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284: Mini-CASP 22 - Single Template
Status: Closed

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beta_helix's picture
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Joined: 05/09/2008
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Secondary structure predictions and more info!

We hope this puzzle will be useful for you to see how important it is to use the alignment tool to find the optimal alignment. Even with the same template, in this case 2fug (chain 5), you can see the very different starting alignments that are possible.

Unfortunately none of the alignments match the N-terminal end of the protein, and the secondary structure predictions (which also used 2fug and the similar structure of 3iam, chain 5 as well) don't help much with that region, but hopefully it will still be somewhat useful:

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 amino acid Phenylalanine at residue 53 is highly predicted to be part of a sheet. However, the Alanine at residue 40 is predicted to have an equal probability of being anything.

For reference, if anyone is interested in the templates:
http://www.rcsb.org/pdb/explore/explore.do?structureId=2FUG
http://www.rcsb.org/pdb/explore/explore.do?structureId=3IAM

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