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673: CASP ROLL Target R0026 - Snake Adenovirus

Closed since about 13 years ago

Advanced Overall Prediction CASP ROLL

Summary

Created
February 01, 2013
Expires
Max points
100
Description

CASP ROLL is back! This latest target is particularly difficult, as we have very low confidence in the templates (you will too once you see them!). We are 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.

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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=70

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 Valine at residue 86 is highly predicted to be part of a sheet. However, the Valine at residue 103 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=2l1t
http://www.pdb.org/pdb/explore/explore.do?structureId=2ggo
http://www.pdb.org/pdb/explore/explore.do?structureId=2va0

beta_helix Staff Lv 1

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.

dflear Lv 1

Are we going to be able to use our saves from this puzzle on the trimer? It would be really cool if we could ;)