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226: Mini-CASP 10 - Freestyle
Status: Closed


Name: 226: Mini-CASP 10 - Freestyle
Status: Closed
Created: 11/25/2009
Points: 100
Expired: 12/02/2009 - 23:00
Difficulty: Advanced
Description: Our 10th 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 give you Rosetta@home predictions for this target as puzzles next week. Until then, good luck freestyle folding! The secondary structure prediction is posted in the puzzle comments.

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beta_helix's picture
User offline. Last seen 1 day 9 hours ago. Offline
Joined: 05/09/2008
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Secondary structure prediction results:

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 122 is highly predicted to be part of a helix. However, the Tyrosine at residue 20 is predicted to have an equal probability of being anything.

Joined: 05/26/2008
Groups: Hold My Beer
This is really good info in

This is really good info in the graph. Is it computationally intensive to produce such a graph? Is there software which I could download and run to get such a graph? Will you make graphs like this available for other puzzles? such as during CASP? It really helps with sculpting questionable areas.

beta_helix's picture
User offline. Last seen 1 day 9 hours ago. Offline
Joined: 05/09/2008
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I'm glad it is useful!

I am using the SAM-server at UC Santa Cruz and usually it takes less than 1 day to get these results back (depending on how many other users are submitting queries to the server).

I have tried to make these graphs available for all the freestyle puzzles, and the plan is to give you as much info as possible during CASP (such as 3D predictions from various servers as well as secondary structure info)

I posted a bit more info about the SAM server here if this helps: http://fold.it/portal/node/986812#comment-5158

Keep in mind, though, these are only predictions and could be incorrect!

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