beta_helix Staff Lv 1
To give you an idea of what one of the possible templates looks like:
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We believe that this CASP target might have a very similar fold.
562: Quick Symmetric CASP10 T0680 Puzzle
Closed since almost 14 years ago
Beginner Beginner Overall Overall Prediction Prediction Symmetry SymmetrySummary
- Created
- May 24, 2012
- Expires
- Max points
- 100
This target is so tough, we aren't even sure of its topology! What we do believe is that one possible topology is a coiled coil (please look at the screenshot of a template in the puzzle comments) so we are giving you this model to fold using symmetry. We will post the other non-symmetric topologies as regular puzzles.
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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
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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, with residues 49-115 predicted to be one long helix!
More info on coiled coils: http://en.wikipedia.org/wiki/Coiled_coil
mottiger Lv 1
if the letter isn't that big, is it more possible that the helix is bended there?
beta_helix Staff Lv 1
Instead of having one long helix, it could actually be a helix bundle: helix-loop-helix-loop-helix as opposed to one long helix.
You'll be able to see that with the next T0680 puzzle, as that is one of the "other topologies" mentioned in the puzzle description.
If you want to look at even more predictions for this target, you can look at ALL the SAM-T08 results for T0680:
http://compbio.soe.ucsc.edu/SAM_T08/results/target08-query-1337702652-9633/summary.html
You can read Part 6 here to understand what everything means:
http://compbio.soe.ucsc.edu/SAM_T08/faq.html
But, for example, if you look at the alpha predictions:
…it does look like it could be 3 helices instead of one long one, but there is no way to know for sure until they solve the structure!