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1488: Small Monomer Design
Status: Closed


Name: 1488: Small Monomer Design
Status: Closed
Created: 02/23/2018
Points: 100
Expired: 03/02/2018 - 23:00
Difficulty: Intermediate
Description: This puzzle challenges players to design a single-chain protein with 65-75 residues. The starting structure has 65 residues, but more can be added at a cost of 23 points per residue. See the puzzle comments for filter 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

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bkoep's picture
User offline. Last seen 2 hours 49 min ago. Offline
Joined: 11/15/2012
Groups: None

Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Ensures that at least 30% of the residues are buried in the core of your design.

Secondary Structure: Checks that no more than 50% of residues are in helices; penalties are incurred if more than 50% of residues form helices.

Secondary Structure Design: Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets; penalizes GLY, ALA, SER, THR in helices.

Residue Count: Penalizes extra residues inserted beyond the starting 65. Players may use up to 75 residues in total.

dbuske's picture
User offline. Last seen 6 hours 41 min ago. Offline
Joined: 09/22/2011
Groups: Beta Folders
I think it is about time you

I think it is about time you set the core existence to a more reasonable and achievable amount.

Susume's picture
User offline. Last seen 1 hour 58 min ago. Offline
Joined: 10/02/2011

I agree a more lenient core filter would help players a lot. There are already sidechains that are in the interior, that the mutate function consistently makes orange, but the core filter colors green and does not give credit for. If we could get credit for those being in the core, you could keep the required ratio of core residues the same but we would have an easier time meeting the filter.

Currently I end up using bands to pull the core closer together to force those sidechains to get counted as core, but those bands are presumably making the protein less realistic in other ways (because they are partially thwarting the score function). If the core filter were as smart (or as lenient) as the mutate function, I could leave the bands off and have a more realistic whole.

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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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