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BETA 60res trimer design test (695) envsmooth=1.2
Status: Closed

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Comments

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

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!

bertro's picture
User offline. Last seen 20 hours 7 min ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
No sidechain bonds with other shadowy parts

These comments are good for all 4 test puzzle as far as I am concerned:

1) Is this a tetramer, I see only 3 chains?

2) My high score is always a chain standing apart from the other two.

3) I cannot maintain any sidechain bonds to the other two part at high score. I have tried to pull them together and make bonds but they all eventually break and disappear at high score.

4) wiggle is not operating as usual, it is sluggish or not responding even at CI=0.

Is it just me or what?

Joined: 05/11/2012
1) Yup, these are trimers

1) Yup, these are trimers like 695 was. Fixed the title of the puzzle

2) I'm not quite sure I understand what you mean by this. Do you mean that your highest score is when the chains are very far apart from each other? Could you post a picture?

3/4) I'll pass this on to the scientists and see what they have to say about it

bertro's picture
User offline. Last seen 20 hours 7 min ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
2/3) Score is higher when

2/3) Score is higher when chains are somewhat apart from each other. I made them make bonds but the bonds mostly vanish as the score gets higher. And SC go back to arginine.

Shared for myself "BETA 60res trimer envsmooth 1.2" @19799.517

I have not been able to improve on it while the 3 parts are more together or apart.

bertro's picture
User offline. Last seen 20 hours 7 min ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
Try also my LOCKED solution

Try also my LOCKED solution at CI=0 W or T:

Shared for myself "BETA 60res trimer envsmooth 1.2 LOCKED" @19744.691

E will move it a bit. But then it is locked again even with Enable Backbone Constraints off.

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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