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491: CASP ROLL Puzzle 2
Status: Closed


Name: 491: CASP ROLL Puzzle 2
Status: Closed
Created: 12/07/2011
Points: 100
Expired: 12/15/2011 - 18:30
Difficulty: Advanced
Description: The second CASP ROLL target, R0002, is 197 residues! We are giving it to you as a freestyle puzzle while we wait for the server predictions to come back. We are providing you with secondary structure predictions that are posted in the puzzle comments and included (only the strong predictions) in the starting structure as well. Again, the deadlline isn't until February!
Categories: Overall, Prediction

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beta_helix's picture
User offline. Last seen 2 weeks 5 days ago. Offline
Joined: 05/09/2008
Groups: None
Please try to use these secondary structure predictions:

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 132 is highly predicted to be part of a sheet. However, the Valine at residue 192 is predicted to be anything.

Joined: 06/17/2010

How important is to use predicted structure?
Is this prediction very accurate? I mean that predicted sheet can be longer or shorter by 1-2 residues but it is "for sure" there?

beta_helix's picture
User offline. Last seen 2 weeks 5 days ago. Offline
Joined: 05/09/2008
Groups: None
It's tough since they are just predictions.

I would use them as suggestions and would trust the higher confidence predictions (the tallest letters), but would definitely NOT fix the structure based solely on these predictions.

What these secondary structure predictions tell us is that, most likely, this structure isn't a bunch of helices!

Joined: 06/17/2010
"Most likely"

are key words there then :)

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