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551: Pre-CASP blind Alignment Puzzle 3
Status: Closed

Summary

Name: 551: Pre-CASP blind Alignment Puzzle 3
Status: Closed
Created: 04/28/2012
Points: 100
Expired: 05/08/2012 - 14:00
Difficulty: Advanced
Description: Here is another blind Template-Based Modeling target to work on. This target is 153 residues and we are again giving you the top-predicted template from 3 different alignment programs (you'll notice that two of them are identical templates, but slightly different alignments) The secondary structure predictions will be posted in the puzzle comments soon.
Categories: Overall, Prediction

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Comments

Joined: 05/09/2008
Groups: None
Delay with the secondary structure predictions:

The SAM-T08 server had a power failure last Thursday and hasn't recovered yet.
I will post them as soon as SAM-T08 is back up and running.

Joined: 05/09/2008
Groups: None
until the SAM-T08 server comes back...

Here are some other secondary structure predictions (that are sadly not as easy to look at):

H = helix
E = sheet
C = loop (or coil)

The higher the number at the top of each position, the higher the probability of that specific secondary structure for that amino acid.

For example, the Phenylalanine at residue 10 is mostly predicted to be part of a helix (an H with a 8 above it). However, the Phenylalanine at residue 55 is predicted to be in a sheet (an E with a 9 above it).

Joined: 05/09/2008
Groups: None
Here are the secondary structure predictions FINALLY:

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 88 is highly predicted to be part of a helix. However, the Valine at residue 32 is predicted to be anything.

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