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 amino acid Leucine at residue 61 is highly predicted to be part of a sheet. However, the Proline at residue 30 is predicted to have an equal probability of being anything!
Looks like you might have to unravel any helices!
It seems to me - being a newbie and all - that this is exactly the kind of thing that we should not pay attention to as human folders.
We can't beat the number crushers at Rosetta et al using statistics, our advantage is the ability to look for patterns beyond statistics.
Essentially, we're looking for harmony and beauty, as far as this makes sense in this entirely novel discipline of visual protein folding?
Thanks for bringing this up OmniDude, this is exactly why we are running the Mini-CASP 15 - Freestyle A & B puzzles: so we can see how much the secondary structure predictions help you.
It could be the case that giving no guidance results in the best human predictions, as you say, but it could also be true that the search space is so large (which is why even all the number crushing currently done by Rosetta@home is not enough) that narrowing the search space so that humans don't have to focus on incorrect topologies might help!
We'll find out when the native structure is released!
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we would like to see how well you can do without any secondary structure predictions first, and then we will post the predictions for you here.