puzzle picture
1619: Symmetric Trimer Design: Hydrogen Bond Networks
Status: Closed

Summary

Name: 1619: Symmetric Trimer Design: Hydrogen Bond Networks
Status: Closed
Created: 01/03/2019
Points: 0
Expired: 01/11/2019 - 23:00
Difficulty: Advanced
Description: Note: This puzzle was closed early due to an error that prevented players from opening the puzzle. The puzzle has been reposted as Puzzle 1619b.

This symmetric design puzzle has C3 symmetry, with three symmetric chains. The H-bond Network Objective 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!
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Comments

bkoep's picture
User offline. Last seen 22 hours 12 min ago. Offline
Joined: 11/15/2012
Groups: None
Objectives

Core Existence: Monomer (max +3000)
Ensures that at least 21 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 +4650)
Ensures that at least 72 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.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

Joined: 12/01/2010
Groups: Beta Folders
I get a message when opening

I get a message when opening this puzzle and it remains stuck on loading.

Anchor residue 91 is not rooted at pose.total_residue() 77

Joined: 11/18/2012
Groups: None
Same here. Anchor residue 91

Same here. Anchor residue 91 is not rooted at pose.total_()77

crpainter's picture
User offline. Last seen 1 day 19 hours ago. Offline
Joined: 09/19/2010
Groups: Contenders
Puzzle. won't load

"Anchor residue 91 is not rooted at pose.total_residue() 77"

NinjaGreg's picture
User offline. Last seen 1 day 18 hours ago. Offline
Joined: 05/21/2010
Groups: Go Science
Same here (mac).

Here's the error dialog:

Joined: 06/06/2013
Groups: Gargleblasters
tentative about even trying this

The last trimer puzzle crashed several times mid script. Once it was running local quake with mutate, once I think dremix. It was very frustrating as it limited the time I had to work with any shape I tried. Might be too big for my machine

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bkoep's picture
User offline. Last seen 22 hours 12 min ago. Offline
Joined: 11/15/2012
Groups: None
Puzzle reposted

Thanks all for the prompt feedback! The corrected puzzle has been reposted here.

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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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