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1279: 85 Residue Monomer Design: Helical Bundles
Status: Closed


Name: 1279: 85 Residue Monomer Design: Helical Bundles
Status: Closed
Created: 09/01/2016
Points: 100
Expired: 09/08/2016 - 23:00
Difficulty: Intermediate
Description: This is a basic 85 residue design puzzle with no secondary structure filter—helical bundles welcome! The Ideal Loops Filter is meant to encourage the use of the Ideal Loops that are displayed in the Rama Map. 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 1 hour 5 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 Design: Penalizes all CYS residues. Penalizes GLY, ALA, and PRO residues in helices and sheets.

Residue Count: Penalizes extra residues inserted beyond the 85 residue limit. Players may insert up to 10 extra residues.

Ideal Loops: Penalizes loops that do not conform to preferred ABEGO patterns. Use Auto Structures to see which residues count as "loops."

Joined: 02/08/2012
Groups: None
Residue Count

I don't get it. If we're given the freedom to insert residues, why are we being penalized? Wouldn't it make more sense to take away the ability to insert residues?

This is just something that I've been wondering for a long time. If this is the wrong place to say this, my deepest apologies.

Joined: 06/06/2013
Groups: Gargleblasters
residue add/subtract can be useful

Drum -- I might use this to tweak the length of helices, sheets or loops easily and adjust without redoing whole fold. Since I'm slow at hand folding, I might add somewhere and subtract elsewhere. Can leave an ideal loop in place if I manage to find one :)

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