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674: CASP ROLL Target R0027 - Turkey Adenovirus

Closed since about 13 years ago

Advanced Overall Prediction CASP ROLL

Summary

Created
February 01, 2013
Expires
Max points
100
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.

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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/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).
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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.

beta_helix Staff Lv 1

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.