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1613: Symmetric Dimer Design: Hydrogen Bond Networks
Status: Closed

Summary

Name: 1613: Symmetric Dimer Design: Hydrogen Bond Networks
Status: Closed
Created: 12/21/2018
Points: 100
Expired: 12/28/2018 - 23:00
Difficulty: Advanced
Description: This symmetric design puzzle has C2 symmetry, with two 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

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Comments

bkoep's picture
User offline. Last seen 11 hours 17 min ago. Offline
Joined: 11/15/2012
Groups: None
Objectives

Core Existence: Monomer (max +2800)
Ensures that at least 28 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 +3400)
Ensures that at least 68 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.

spvincent's picture
User offline. Last seen 9 hours 30 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
It seems there's a recent

It seems there's a recent paper from the Baker group on this subject summarized here:

https://www.sciencedaily.com/releases/2018/12/181219133219.htm

It looks like Rosetta can now design these hydrogen bond networks to a high level of accuracy. Which is great of course but does leave me wondering what they're hoping to learn from this current crop of dimer puzzles

bkoep's picture
User offline. Last seen 11 hours 17 min ago. Offline
Joined: 11/15/2012
Groups: None
Good question!

I'm sorry I didn't get to around to answering this before the puzzle closed!

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.

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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