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1681: Symmetric Trimer Design: 80 Residues

Closed since almost 7 years ago

Intermediate Overall Design Symmetry

Summary

Created
May 31, 2019
Expires
Max points
100
Description

This symmetric design puzzle has C3 symmetry, with three symmetric chains. There is no H-bond Network Objective in this puzzle, so the interface can be completely nonpolar (orange sidechains). 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. 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!

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Comments

bkoep Staff Lv 1

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

Core Existence: Complex (max +4200)
Ensures that at least 84 residues are buried in the core of the entire complex (including the interface between monomer units).

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.

Bautho Lv 1

It is always a pity when you are not able to delete residues at one end and stick them to the other end of the protein :(

bkoep Staff Lv 1

This is a long-standing complaint, and we hope to correct it soon!

For obscure reasons, it is slightly more complicated to implement this for symmetry puzzles (insertions and deletions are more straightforward in the monomer design puzzles). But there are ways around this, and it's on our to-do list!