puzzle picture
487: CASP ROLL Puzzle 1
Status: Closed

Summary

Name: 487: CASP ROLL Puzzle 1
Status: Closed
Created: 12/01/2011
Points: 100
Expired: 12/11/2011 - 23:59
Difficulty: Advanced
Description: This is the first CASP ROLL target: R0001. 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 in the starting structure as well. It's 183 residues long, but get used to this protein because it's deadlline isn't until February!
Categories: Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 4 days 7 hours 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 3 is highly predicted to be part of a sheet. However, the Valine at residue 116 is predicted to be anything.

Joined: 06/25/2011
Groups: Androids
Regarding the W-Y-I sequence at 26-28...

It seems like the placement and identity of the other segments force that sequence to be a loop, rather than a (as predicted by the server to be slightly more likely) sheet.

B_2's picture
User offline. Last seen 3 years 1 day ago. Offline
Joined: 11/29/2008
Groups: None
Is this a previously unsolved

Is this a previously unsolved protein, or is this just enhancing a known or previously predicted structure?

I can't tell from the CASP site, since 90% of what's on there is gibberish to a layman.

beta_helix's picture
User offline. Last seen 4 days 7 hours ago. Offline
Joined: 05/09/2008
Groups: None
CASP ROLL just started last week

so these are all blind targets where the natives have not been released yet.
Here is the target list so you can see when the expiration deadlines are: http://predictioncenter.org/casprol/targetlist.cgi

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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