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

Groups

RankGroupScorePoints
1Richard Dawkins Foundation11,500100
2Contenders11,38572
3Void Crushers11,20550
4Russian team10,91034
5Another Hour Another Point10,78923
6SETI.Germany10,77615
7Natural Abilities10,44710
8Free-DC10,3786
9L'Alliance Francophone10,3454
10Crunching Family10,3242
11Mad Lab10,2352
12Team New Zealand9,8021
13CryptoFolders9,7631
14Mac Users9,7001
15sfb5798,9721
16Boinc.be8,1851
17Team China7,5021
18Ukraine7,4011
19DSN @ Home7,3951
20test_group16,1691
21Aotearoa's Assassins01
22Dutch Power Cows01


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beta_helix's picture
User offline. Last seen 15 hours 58 min ago. Offline
Joined: 05/09/2008
Groups: None
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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