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1485: Extra Large Monomer Design
Status: Closed

Summary

Name: 1485: Extra Large Monomer Design
Status: Closed
Created: 02/16/2018
Points: 100
Expired: 02/23/2018 - 23:00
Difficulty: Intermediate
Description: This puzzle challenges players to design a single-chain protein with 90-125 residues. The starting structure has 90 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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1Gargleblasters10,903100
2Beta Folders10,85863
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Comments

bkoep's picture
User offline. Last seen 3 hours 11 min ago. Offline
Joined: 11/15/2012
Groups: None
Filters

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

Core Existence: Ensures that at least 35% 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 90. Players may use up to 125 120 residues in total.

LociOiling's picture
User offline. Last seen 1 hour 41 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
120 segments maximum

The comments say 90 to 125 segments, but I can't add beyond segment 120. That's actually the normal maximum for an "extra large monomer", so we'll assume the 125 was a typo.

bkoep's picture
User offline. Last seen 3 hours 11 min ago. Offline
Joined: 11/15/2012
Groups: None
Typo

You're correct, that was a typo. Thanks for pointing it out! I've amended the comment.

SaraL's picture
User offline. Last seen 5 days 16 min ago. Offline
Joined: 09/20/2011
Groups: Gargleblasters
Broken protein?

I was able to get my protein up to 9826, however after that point the system appeared to 'break'.

Any manner of wiggling other than local would force the protein to come apart and fold to a worse score with negative penalties for loops not scoring high enough and not enough residues in the core.

I tried low/medium power, with clashing importance adjusted from 0.03 to 1.00 - Same result every time.

bkoep's picture
User offline. Last seen 3 hours 11 min ago. Offline
Joined: 11/15/2012
Groups: None
Hmm

That's weird. Can you share your solution using the Share with Scientists button, and we'll take a look?

Susume's picture
User offline. Last seen 43 min 15 sec ago. Offline
Joined: 10/02/2011
Remove blueprint constraints?

When a monomer design starts pulling radically out of shape, sometimes it means the "ideal loop" constraints have moved to the wrong spot on the protein due to deleting/adding segments. Open blueprint, and if there are white rectangles on the sequence of letters, drag the rectangles off. That removes the constraints and lets your protein wiggle more freely.

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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, Microsoft, Adobe, RosettaCommons