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397: Quest to the Native Design
Status: Closed


Name: 397: Quest to the Native Design
Status: Closed
Created: 02/02/2011
Points: 100
Expired: 02/07/2011 - 23:00
Difficulty: Beginner
Description: This is the first Quest to the Native Design Puzzle. As mentioned in the blog (http://fold.it/portal/node/989141) we can identify an interaction between a disembodied sidechain and the protein surface and we then want to figure out a backbone conformation that can harbor that sidechain. This quest to the native is based on Puzzle 389: Design the Interface 5 (which you have seen in Gallery Mode). We want to see if this new disembodied sidechain representation (Trp 130) works well for you.

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beta_helix's picture
User offline. Last seen 2 weeks 2 days ago. Offline
Joined: 05/09/2008
Groups: None
Comments on the new disembodied sidechain representation?

Please let us know what you think about the new disembodied sidechain representation. Thanks for your feedback!

Also note that this puzzle will close a day earlier than usual since it shouldn't take much time to work on.

spmm's picture
User offline. Last seen 8 weeks 17 hours ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
matching the guide does not seem to score much

Having matched the guide and the sidechains which are unambiguous from the 'shadow' my score moved alarming lower even after rebuilds stabilising etc to improve it.
Having looked at a screen shot of a high scoring solution it is very different to the guide.
So why not just give us the formation shown in the guide and constraints to start with so we can improve from there.
My low score may of course be just my problem but closer to a 'guide' should reult in higher score or one just ignores the guides.
Bit confued by the intent.

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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, Boehringer Ingelheim, RosettaCommons