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1689: Symmetric Dimer Design: 80 Residues
Status: Closed

Summary

Name: 1689: Symmetric Dimer Design: 80 Residues
Status: Closed
Created: 06/20/2019
Points: 100
Expired: 06/28/2019 - 23:00
Difficulty: Intermediate
Description: This symmetric design puzzle has C2 symmetry, with two symmetric chains. No more than 50% of residues may form helices, and all loops must match one of the Ideal Loop Building Blocks found in the Blueprint tool. We've omitted the "Core Exists: Complex" objective to simplify the puzzle, but we still expect that designs with a strong hydrophobic interface (orange sidechains) will score best. See the puzzle comments for Objective 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 48 min ago. Offline
Joined: 11/15/2012
Groups: None
Objectives

Core Existence: Monomer (max +2400)
Ensures that at least 24 residues are buried in the core of the monomer unit.

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA, SER, THR in 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.

Secondary Structure (max +500)
No more than 50% of residues may form helices. Extra helices are penalized at 10 points per residue.

frood66's picture
User offline. Last seen 9 hours 19 min ago. Offline
Joined: 09/20/2011
Groups: Marvin's bunch
filters

Is this gonna be reposted with a complex core filter? If not - could FC explain why such a filter is not used in this puzzle? The reasoning?

bkoep's picture
User offline. Last seen 11 hours 48 min ago. Offline
Joined: 11/15/2012
Groups: None
No repost

We think the Complex Core Objective is unnecessary, so we're trying a few puzzles without it. It is still important that the two chains come together to create a buried interface. But it seems like these good solutions already score better than bad solutions (where the two chains are separated), even without the Complex Core bonus.

In general, we prefer not to use Objectives if we can help it. Objectives require some extra computation, which can slow down gameplay (some Objectives are worse than others). This puzzle should run slightly faster without the Complex Core Objective.

Objectives can also lead to some funny behavior with tools like Wiggle and Shake, which aren't really "aware" of objectives. These tools are good at optimizing the base Foldit score, but they can inadvertently cause an Objective to fail, resulting in a net loss.

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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