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197: Mini-CASP 3-Freestyle

Closed since over 16 years ago

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Summary

Created
September 16, 2009
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Max points
100
Description

The third Mini-CASP target is another de-novo (or ab-initio) target. This means that there is no solved structure that has a similar sequence that we can start our predictions from. This is exciting because template-free targets are rare (in CASP8 only 11 of the 128 targets were free-modeling targets) so we are lucky to be able to predict this. Since we have no idea where to even start, we are giving you an extended chain to see what you come up with. This might not be easy, so we will release Rosetta predictions for this target as puzzles early next week. Until then, good luck freestyle folding! As suggested in the feedback (http://fold.it/portal/node/986548#comment-4998) we will post the secondary structure prediction in the puzzle comments.

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Comments

beta_helix Staff Lv 1

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 Valine at residue 60 is highly predicted to be part of a beta sheet. However, the Valine at residues 51 is predicted to have an equal probability of being part of a sheet or part of a loop (so it's probably not a helix).

Nicky666 Lv 1

Thanks for that, it already helped :)

btw, maybe a stupid question, but how are these secondary structures predicted?

Nicky666 Lv 1

This will take some more research tomorrow, as it doesn't read like a bedtime story…I didn't even know I wanted to know anything about Hidden Markov Models, LOL.

I'll have fun learning though, no doubt, your links are very much appreciated!