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673: CASP ROLL Target R0026 - Snake Adenovirus
Status: Closed

Summary

Name: 673: CASP ROLL Target R0026 - Snake Adenovirus
Status: Closed
Created: 01/31/2013
Points: 100
Expired: 02/15/2013 - 18:00
Difficulty: Advanced
Description: CASP ROLL is back! This latest target is particularly difficult, as we have very low confidence in the templates (you will too once you see them!). We are providing you with 3 templates for now, and will give you some server predictions once they are released. Feel free to just work off the starting extended chain if you don't trust the alignments. More details about this CASP target are in the puzzle comments.
Categories: CASP ROLL, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 23 hours 51 min ago. Offline
Joined: 05/09/2008
Groups: None
Additional info about this CASP Roll target

Here is the CASP link for this target (showing the amino acid sequence):
http://predictioncenter.org/casprol/target.cgi?id=70

____________________________________________________

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 86 is highly predicted to be part of a sheet. However, the Valine at residue 103 is not predicted to be anything!

The above predictions are already on the starting model (based on the horizontal lines in the above figure).
____________________________________________________

Link to template PDBs:

http://www.pdb.org/pdb/explore/explore.do?structureId=2l1t
http://www.pdb.org/pdb/explore/explore.do?structureId=2ggo
http://www.pdb.org/pdb/explore/explore.do?structureId=2va0

beta_helix's picture
User offline. Last seen 23 hours 51 min ago. Offline
Joined: 05/09/2008
Groups: None
This target will be posted as a trimer in the next round

You may have noticed that the CASP organizers have told us that "The protein is known to form very stable homo-trimers."

We will post this CASP target with symmetry in the next round, when we give you the server predictions as starting models.

Symmetry doesn't currently work with the alignment tool, so there was no way to do that for this puzzle.

dflear's picture
User offline. Last seen 1 year 16 weeks ago. Offline
Joined: 10/08/2012
For the Trimer..

Are we going to be able to use our saves from this puzzle on the trimer? It would be really cool if we could ;)

beta_helix's picture
User offline. Last seen 23 hours 51 min ago. Offline
Joined: 05/09/2008
Groups: None
good question!

I'll see if that is possible... hopefully it is!

beta_helix's picture
User offline. Last seen 23 hours 51 min ago. Offline
Joined: 05/09/2008
Groups: None
:-(

sadly, we won't be able to do this... at least not with the current Foldit client

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