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674: CASP ROLL Target R0027 - Turkey Adenovirus
Status: Closed

Summary

Name: 674: CASP ROLL Target R0027 - Turkey Adenovirus
Status: Closed
Created: 02/01/2013
Points: 100
Expired: 02/18/2013 - 21:00
Difficulty: Advanced
Description: The next CASP ROLL target is another tough one. We are again 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. Due to the size, we're giving you a few extra days to work on this one.
Categories: CASP ROLL, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 6 hours 2 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=71

____________________________________________________

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 Valines at residues 106 & 120 are highly predicted to be part of a sheet. However, the Valine at residue 57 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=3i12
http://www.pdb.org/pdb/explore/explore.do?structureId=3gdb
http://www.pdb.org/pdb/explore/explore.do?structureId=2rct
____________________________________________________

This target will also 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.

Joined: 08/24/2011
Slow=unfun

Too bad we'll have to replay this puzzle. Old configs are too challenged for this :/

beta_helix's picture
User offline. Last seen 6 hours 2 min ago. Offline
Joined: 05/09/2008
Groups: None
This CASP ROLL target might be too large for symmetry

Indeed, Jean-Bob... if this puzzle is already quite slow as a monomer, it might not be feasible as a trimer! :-(

We'll see how the version of 673 with symmetry goes before we repost this one with symmetry.

Worst-case, we can always post it as a Contest or as a Bonus Puzzle for anyone interested in trying it out with symmetry.

gramps's picture
User offline. Last seen 5 years 16 weeks ago. Offline
Joined: 12/16/2010
new public Recipe: 674 jpred structs

http://fold.it/portal/recipe/45367

Some differences from the above, for example a large-ish C-end Helix(149,156)

beta_helix's picture
User offline. Last seen 6 hours 2 min ago. Offline
Joined: 05/09/2008
Groups: None
Puzzle has been extended by a few hours
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