226: Mini-CASP 10 - Freestyle

Closed since over 16 years ago

Summary

• Created: November 25, 2009
• Expires: December 02, 2009 at 23:00 UTC
• Max points: 100

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.

Top groups

• 1. Richard Dawkins Foundation 100 pts. 10,837
• 2. Void Crushers 85 pts. 10,830
• 3. Deleted group pts. 10,828
• 4. Russian team 60 pts. 10,693
• 5. Contenders 49 pts. 10,608
• 6. Deleted group pts. 10,401
• 7. SETI.Germany 33 pts. 10,349
• 8. ExPitneyFolders 27 pts. 10,204
• 9. Deleted group pts. 10,142
• 10. Natural Abilities 17 pts. 10,142

Top soloists

• 1. aap 100 pts. 10,837
• 2. steveB 98 pts. 10,830
• 3. Steven Pletsch 95 pts. 10,823
• 4. Mark- 92 pts. 10,608
• 5. Madde 89 pts. 10,582
• 6. Enzyme 87 pts. 10,563
• 7. BootsMcGraw 84 pts. 10,533
• 8. vertex 82 pts. 10,520
• 9. TheGUmmer 79 pts. 10,468
• 10. marie_s 77 pts. 10,460

Comments

[beta_helix]

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.

[Steven Pletsch]

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]

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!