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564: CASP10 Target T0680
Status: Closed

Summary

Name: 564: CASP10 Target T0680
Status: Closed
Created: 05/26/2012
Points: 100
Expired: 06/03/2012 - 23:59
Difficulty: Advanced
Description: As mentioned in Puzzle 562, we are uncertain of the topology for T0680. We are providing you with 5 templates that span two very different topologies (in addition to the symmetry one in 562) before providing you with the server predictions that will be released next week. Please try out BOTH topologies! More details in the puzzle comments.
Categories: CASP10, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 3 hours 22 min 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=77
____________________________________________________

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.

You can see that this protein is pretty much predicted to be helical, the question is whether residues 49-115 form a few helices or one long helix
(as in the suggested topology for Puzzle 562:
http://fold.it/portal/node/992747#comment-17661) which is the same CASP10 target.

____________________________________________________

Link to template PDBs, where you can see two distinct topologies:

Coiled coil:
http://www.pdb.org/pdb/explore/explore.do?structureId=2v1y
http://www.pdb.org/pdb/explore/explore.do?structureId=2ysu

Helix Bundle:
http://www.pdb.org/pdb/explore/explore.do?structureId=2v6x
http://www.pdb.org/pdb/explore/explore.do?structureId=3u8v
http://www.pdb.org/pdb/explore/explore.do?structureId=256b

Our hope is that one of these two topologies is correct (or the symmetry one in Puzzle 562) so please make sure to try out both topologies as much as possible for this puzzle.

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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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