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1602: Symmetric Dimer Design

Closed since over 7 years ago

Intermediate Overall Design Symmetry

Summary

Created
November 23, 2018
Expires
Max points
100
Description

This symmetric design puzzle has C2 symmetry, with two symmetric chains. There is no H-bond Network Objective in this puzzle, so the interface can be completely nonpolar (orange sidechains). However, there other stringent objectives in effect: solutions may have no more than 50% of residues in 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 +2500)
Ensures that at least 25 residues are buried in the core of the monomer unit.

Core Existence: Complex (max +3100)
Ensures that at least 62 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 and helices

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

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.

Skippysk8s Lv 1

just a note that some of my "ideal loops" showed up as non-ideal even with blueprint tool holding them locked…. I think it is me, but it is frustrating

bkoep Staff Lv 1

Can you share those solutions with us? Or let us know which Building Blocks are setting off the Ideal Loops objective?