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626: Slightly Different Freestyle Puzzle
Status: Closed

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beta_helix's picture
User offline. Last seen 6 days 8 hours ago. Offline
Joined: 05/09/2008
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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.

For example, the Valines at residues 7 & 68 are highly predicted to be part of a helix. However, the Valines at residues 31, 35, 43, 52, 88, 97, 101 & 120 are highly predicted to be in a sheet.

spmm's picture
User offline. Last seen 44 weeks 2 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
very stiff

this is really stiff to move even on CI= 0.3

beta_helix's picture
User offline. Last seen 6 days 8 hours ago. Offline
Joined: 05/09/2008
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Thank you for the feedback, spmm

This is exactly what we are trying to find out by giving you a slightly different scoring function.
We will repost this as a Quick Puzzle with the regular scoring function for comparison.

Joined: 05/19/2009
Groups: Contenders
scoring == stiffness ?

In what way is a scoring function related to the stiffness of a structure ? I would think that the stiffness is not depending on a score. Can you please explain this ?

beta_helix's picture
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Joined: 05/09/2008
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I agree that it should not be dependent!

It is very strange that this puzzle would be more stiff than any other freestyle extended chain that we give you (since they are generated in the exact same way).

The only difference here (other than the amino acid sequence, obviously) is the score function.

It will be interesting to see if reposting the exact same puzzle with the traditional Foldit scoring function gets rid of this stiffness.

If not, then there might be something else going on!

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons