puzzle picture
718: Hand-Folding Flu Puzzle: Design the Core
Status: Closed

Summary

Name: 718: Hand-Folding Flu Puzzle: Design the Core
Status: Closed
Created: 05/23/2013
Points: 100
Expired: 05/30/2013 - 19:00
Difficulty: Intermediate
Description: In this puzzle we are trying to create a new better core for one of the Baker Lab flu proteins. We know what the key interface residues should be, that's why you can't change them, but a new core may increase the stability of the protein. Ultimately a more stable protein might translate into a better protein therapeutic. We don't want you to drift too far from the initial topology, so this puzzle has an RMSD condition. You might want to mutate the core of the protein before you wiggle to not violate this condition. Because this is a Hand-Folding round, only GUI scripts are allowed and sharing has been disabled. More details about all this in the puzzle comments.
Categories: Design, Hand-Folding, Overall

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Comments

beta_helix's picture
User offline. Last seen 4 days 8 hours ago. Offline
Joined: 05/09/2008
Groups: None
About the RMSD condition

We need you to focus on improving the core of this protein, so we don't want you to change the overall shape of the protein too much.
That is why there is a RMSD condition, where you cannot drift more then 2 Angstroms RMSD from the C-alpha backbone of the starting structure.
You can click on Show in the panel below your Score to see where the starting backbone is.
If you deviate over 2 Angstroms from the start, your score will no longer count.
Because the starting model doesn't have a proper core, if you just wiggle right away it will collapse onto itself and violate the condition. You probably want to manually mutate the core of the protein first, before using wiggle so as not to violate the condition.

This is a Hand-Folding Round:

This round only GUI scripts are allowed and sharing has been disabled. After this puzzle expires, the puzzle will be re-posted and LUA scripts and sharing will be allowed. You'll be able to load in your solutions from this puzzle and use scripting and sharing.

beta_helix's picture
User offline. Last seen 4 days 8 hours ago. Offline
Joined: 05/09/2008
Groups: None
Please try to keep the ends of the protein away from the core!

Once it's up, I will post a link to the log of the Scientist Chat where Baker Lab Scientist Aaron explained how both ends of the protein (residues 270-273 and 314-316) need to be pointing away from the core.

Hopefully the RMSD condition keeps this from happening, and we do not have to add an even more strict RMSD condition to these two ends.

EDIT: transcript is now up:
http://fold.it/portal/node/995205

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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