Foldit

1617: Symmetric Trimer Design: Hydrogen Bond Networks

Closed since about 7 years ago

Summary

Created: December 27, 2018
Expires: January 04, 2019 at 23:00 UTC
Max points: 100

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!

Top groups

1. Contenders
100 pts. 23,499
2. Anthropic Dreams 73 pts. 23,180
3. Gargleblasters 52 pts. 23,139
4. Go Science 36 pts. 23,062
5. Beta Folders 24 pts. 22,942
6. L'Alliance Francophone 16 pts. 22,219
7. Russian team 10 pts. 22,085
8. Void Crushers 6 pts. 22,006
9. Marvin's bunch 4 pts. 21,107
10. HMT heritage 2 pts. 20,693

1. johnmitch Lv 1
100 pts. 23,480
2. Mark- Lv 1 97 pts. 23,419
3. Glen B Lv 1 93 pts. 23,204
4. Galaxie Lv 1 90 pts. 23,179
5. actiasluna Lv 1 86 pts. 23,139
6. toshiue Lv 1 83 pts. 23,062
7. isaksson Lv 1 80 pts. 22,961
8. LociOiling Lv 1 77 pts. 22,930
9. stomjoh Lv 1 74 pts. 22,903
10. crpainter Lv 1 71 pts. 22,776

Comments

bkoep Staff Lv 1

December 27, 2018

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 Staff Lv 1

December 28, 2018

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.