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564: CASP10 Target T0680

Closed since almost 14 years ago

Advanced Overall Prediction

Summary

Created
May 26, 2012
Expires
Max points
100
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.

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Comments

beta_helix Staff Lv 1

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.