puzzle picture
1608: Symmetric Dimer Design: Hydrogen Bond Networks
Status: Closed

Summary

Name: 1608: Symmetric Dimer Design: Hydrogen Bond Networks
Status: Closed
Created: 12/07/2018
Points: 100
Expired: 12/14/2018 - 23:00
Difficulty: Advanced
Description: This symmetric design puzzle has C2 symmetry, with two symmetric chains. The H-bond Network Bonus encourages players to bury H-bond networks at the interface between the two chains. We've doubled the H-bond network bonus, but we'd like players to focus on building networks deep in the core of the protein complex. There are a couple other bonuses 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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2Beta Folders20,58276
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Comments

bkoep's picture
User offline. Last seen 6 hours 14 min ago. Offline
Joined: 11/15/2012
Groups: None
Objectives

Core Existence: Monomer (max +1900)
Ensures that at least 19 residues are buried in the core of the monomer unit. The threshold of "buriedness" between core and surface residues is more stringent than usual, so residues may have to be "extra buried" to be counted toward the core.

Core Existence: Complex (max +2100)
Ensures that at least 42 residues are buried in the core of the entire complex (including the interface between monomer units).

HBond Network
Rewards networks that comprise at least three hydrogen bonds involving core residues. Networks must be at least 70% satisfied (i.e. 70% of all oxygens and polar hydrogens in a network must make a hydrogen bond).

SS Design (max +500)
Prohibits all CYS residues. Prohibits GLY, ALA residues in sheets and helices.

toshiue's picture
User offline. Last seen 9 hours 33 min ago. Offline
Joined: 01/31/2016
Groups: Go Science
two 1607s

this one is really 1608?

bkoep's picture
User offline. Last seen 6 hours 14 min ago. Offline
Joined: 11/15/2012
Groups: None
Yes!

Sorry for the oversight, this has been corrected!

dbuske's picture
User offline. Last seen 11 hours 55 min ago. Offline
Joined: 09/22/2011
Groups: Beta Folders
2nd chain

I cannot find the 2nd chain, then I lost the 1st chain.
Q does not work to find the 1st chain.

Joined: 01/24/2016
Groups: None
That has happened to me in

That has happened to me in the past. If the 2 chains get too far apart, then Q will not work. Q will center the midpoint of the 2 chains. Also, if you rotate them like that, the "dimming" lighting effect will make the 1st chain disappear.

Either move the chain so that the ends furthest apart are nearer;

from: 111111111111111 2222222222222222

to: 111111111111111
222222222222222

at the start of the game, or use a band to anchor one end of chain 1, before running any recipes.

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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