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566: CASP10 Target T0691
Status: Closed

Summary

Name: 566: CASP10 Target T0691
Status: Closed
Created: 05/30/2012
Points: 100
Expired: 06/09/2012 - 12:00
Difficulty: Intermediate
Description: The seventh CASP10 target is not an easy one, as it's 163 residues and we don't have any alignments for the first 18 residues. We are providing you with 5 different templates, but all of them have a similar topology (that we hope is the correct one!). We will provide you with server predictions once they are released. More details about this CASP target are in the puzzle comments.
Categories: CASP10, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 6 days 20 hours ago. Offline
Joined: 05/09/2008
Groups: None
Additional info about this CASP target

Here is the CASP link for this target (showing the amino acid sequence):
http://predictioncenter.org/casp10/target.cgi?id=92
____________________________________________________

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 Leucines at residues 10, 14 & 15 are highly predicted to be in a helix. However, the Leucines at residues 62, 115, 125 & 127 are predicted to be sheets.
____________________________________________________

Link to template PDBs:

http://www.pdb.org/pdb/explore/explore.do?structureId=1gt1
http://www.pdb.org/pdb/explore/explore.do?structureId=1ew3
http://www.pdb.org/pdb/explore/explore.do?structureId=1pm1
http://www.pdb.org/pdb/explore/explore.do?structureId=1gm6
http://www.pdb.org/pdb/explore/explore.do?structureId=3qzk

beta_helix's picture
User offline. Last seen 6 days 20 hours ago. Offline
Joined: 05/09/2008
Groups: None
The first 18 residues are predicted to be in a helix

The N-terminal region of this CASP10 target is unaligned to any of the 5 templates we have given you, but it is predicted to be helical.

Here is a hint to easily make a helix (if that is what you want to attempt):

The rebuild tool takes structure assignment into account, so you can set the secondary structure to helix and then Rebuild. Foldit will then make a helix out of that region.

mimi's picture
User offline. Last seen 4 days 35 min ago. Offline
Joined: 11/17/2008
Groups: Contenders
is there a problem?

puzzle isn't actually appearing as an option on the list

beta_helix's picture
User offline. Last seen 6 days 20 hours ago. Offline
Joined: 05/09/2008
Groups: None
Sorry, was waiting on the update to devprev:

It should be up now, we were waiting on the update to devprev:
http://fold.it/portal/node/992806

specifically this bugfix:
Alignment Tool -
* Secondary structures are now assigned when threading

since this will make it easier when threading the template for this CASP10 target, due to the beta barrel topology: http://en.wikipedia.org/wiki/Beta_barrel

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