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BETA 60res trimer design test (695) score13
Status: Closed

Summary

Name: BETA 60res trimer design test (695) score13
Status: Closed
Created: 04/02/2013
Points: 0
Expired: 04/09/2013 - 23:00
Difficulty: Intermediate
Description: This puzzle is testing weights for the envsmooth (smoothed environment) score term. What this term does is look at the environment around each amino acid and determine if it is statistically similar to the environment found in similar amino acids in native proteins. In earlier design puzzles, this score term was not used. In puzzle 695 we added this score term and weighted it very highly (at 3.0). We are now testing out smaller values for this score term. This puzzle has envsmooth=0.56 along with some other changes to the scoring function (codename: score13) You will be able to load in your solutions from 695, and also load back/forth between the 4 different devprev puzzles that are testing envsmooth.
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Comments

tamirh's picture
User offline. Last seen 6 years 43 weeks ago. Offline
Joined: 05/11/2012
Mutate All

Note: Hitting mutate all when the protein is still an extended chain will still give you arginine. If mutating when the protein is actually folded only gives you arginine then please let us know.

Slight differences in what wiggle and mutate do when the protein is an extended chain are expected. If you could play around with the protein more and see if it does what you expect we would appreciate it.

List of all puzzles with score function variations for this 60 residue tetramer:
http://fold.it/portal/node/994883
http://fold.it/portal/node/994884
http://fold.it/portal/node/994885
http://fold.it/portal/node/994886

tamirh's picture
User offline. Last seen 6 years 43 weeks ago. Offline
Joined: 05/11/2012
What to test

Please use the techniques you've learned from other symmetric design puzzles to see how the different versions of this BETA puzzle react. What we're interested in is having the highest value of envsmooth possible without adversely affecting the tools you use.

One other thing to keep in mind is how puzzle http://fold.it/portal/node/994886 reacts differently also. There are more variables that are changed in this version, not just envsmooth.

Thanks for all the help!

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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