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

Soloists

RankPlayerGroupScorePoints
101ourtown 70 1855  7,9941
102xedr 70 1855  7,7751
103Glorf97 70 1855  7,5971
104Tamison 70 1855 Richard Dawkins Foundation7,5941
105Fr0sty 70 1855  7,5671
106djag 70 1855  7,5071
107zglloo 70 1855 Team China7,5021
108foldingit 70 1855  7,5001
109Elfi 70 1855  7,4981
110anne romaine 70 1855  7,4951
111Dianeruth 70 1855  7,4491
112xabxs 70 1855  7,4211
113Sergyg 70 1855 Ukraine7,4011
114aspadistra 70 1855 DSN @ Home7,3951
115Lockhart 70 1855  7,3941
116Radagast 70 1855 7,3931
117lilovip 70 1855  6,7781
118sirenbrian 70 1855 6,7691
119SniperSmiley 70 1855  6,6331
120robotic emu 70 1855  6,4071
121r7iwai 70 1855  6,3831
122test_account1 70 699 test_group16,1691
123umfgzahr 70 1855  5531
124rdtsc 70 1855  01
125 David Baker 70 1855  01


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beta_helix's picture
User offline. Last seen 1 day 1 hour ago. Offline
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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