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1090: 80 Residue Symmetric Dimer Design
Status: Closed

Summary

Name: 1090: 80 Residue Symmetric Dimer Design
Status: Closed
Created: 05/19/2015
Points: 100
Expired: 05/26/2015 - 23:00
Difficulty: Intermediate
Description: This puzzle again uses separate "Core Existence" filters for the monomer unit and the symmetric complex. Click the "Show" checkbox beneath the Core Existence filter to see which residues have been identified as Core (orange), Boundary (green), or Surface (blue). There are several other filters in effect; see the puzzle comments for details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!
Categories: Design, Overall, Symmetry

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Comments

bkoep's picture
User offline. Last seen 18 hours 5 min ago. Offline
Joined: 11/15/2012
Groups: None
Filters

Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Monomer: Ensures that at least 22 residues are buried in the core of the monomer unit.

Core Existence: Complex: Ensures that at least 50 residues are buried in the core of the entire complex (including the interface between monomer units).

Fragment Score: Scans for parts of your design that are unlikely to fold up naturally. Use Rebuild and Remix tools to fix these regions of your design!

Secondary Structure Design: Penalizes all CYS residues. Penalizes GLY, ALA, and PRO residues in helices and sheets.

Joined: 09/24/2012
Groups: Go Science
strange

I've a solution with all bonus ok including core existence complex BUT my 2 monomers are still far away from each other ...

Joined: 10/30/2012
Groups: Beta Folders
me too

me too

bkoep's picture
User offline. Last seen 18 hours 5 min ago. Offline
Joined: 11/15/2012
Groups: None
Thanks for the feedback!

This came up in Puzzle 1068, as well:
http://fold.it/portal/node/2000548#comment-30118

If your monomer units are especially well-packed, it is possible to pass the "Core Existence: Complex" filter without designing an interface. We've intentionally set a low threshold here to allow more diversity in designs.

At some point, we might change the filter behavior so this isn't possible; but for the time being, I encourage you to design an interface in spite of your filter bonus!

Joined: 04/10/2015
Groups: Beta Folders
Just a thought maybe in

Just a thought maybe in future puzzle you can increase the bonus in the Core Existence: Complex for interaction and give more freedom with a lower requirement for Core Existence: Monomer.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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