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1617: Symmetric Trimer Design: Hydrogen Bond Networks
Status: Closed

Summary

Name: 1617: Symmetric Trimer Design: Hydrogen Bond Networks
Status: Closed
Created: 12/27/2018
Points: 100
Expired: 01/04/2019 - 23:00
Difficulty: Advanced
Description: 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!
Categories: Design, Overall, Symmetry

Top Groups

RankGroupScorePoints
1Contenders23,499100
2Anthropic Dreams23,17973
3Gargleblasters23,13852
4Go Science23,06236
5Beta Folders22,94224

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1johnmitch 81 10  23,479100
2Mark- 57 45 Contenders23,41997
3Glen B 81 44  23,20393
4Galaxie 2 2 Anthropic Dreams23,17890
5actiasluna 11 3 Gargleblasters23,13886


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Comments

bkoep's picture
User offline. Last seen 16 hours 53 min ago. Offline
Joined: 11/15/2012
Groups: None
Objectives

Core Existence: Monomer (max +2100)
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 +3600)
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.

bkoep's picture
User offline. Last seen 16 hours 53 min ago. Offline
Joined: 11/15/2012
Groups: None
Rosetta-designed networks

On the previous symmetry puzzle, Foldit player spvincent asked a question about H-bond networks designed by Rosetta vs. Foldit players. Unfortunately we didn't get to answer the question until after the puzzle closed, but I wanted to make sure players saw our answer, which is pasted below:

The Rosetta tool for finding H-bond networks is very good at mutating residues to design a network onto a fixed backbone. The typical Rosetta workflow is to generate a library of protein backbones, and then look for H-bond networks in each backbone. Most backbones cannot accommodate a fully-satisfied network—but that's okay, as long as we have a large number of backbones to scan through.

We think that Foldit players might be able to find H-bond networks with modifications to the protein backbone. If players happen upon a backbone that supports an almost-satisfied network, then players might be able to see how the backbone could be adjusted to complete the network. Rosetta isn't very good about imagining what could be (it only sees the exact backbones that are fed to it), so this could be a complementary approach to the design of H-bond networks.

Joined: 09/21/2011
Groups: Void Crushers
Objectives wrong

I see 2 SS design boxes and no Ideal loop box

vakobo's picture
User offline. Last seen 14 hours 3 min ago. Offline
Joined: 06/05/2008
Groups: Russian team
I got Monomer bonus more than

I got Monomer bonus more than 2100 and Complex bonus more than 3600

Joined: 09/21/2011
Groups: Void Crushers
Extra bonus if satisfied

You get 160 extra if all are there I think

frood66's picture
User offline. Last seen 4 hours 31 min ago. Offline
Joined: 09/20/2011
Groups: Marvin's bunch
plus 160 on complex core

plus 160 on complex core bonus also

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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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