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1610: Symmetric Dimer Design: Hydrogen Bond Networks

Closed since over 7 years ago

Advanced Overall Design Symmetry

Summary

Created
December 14, 2018
Expires
Max points
100
Description

This symmetric design puzzle has C2 symmetry, with two symmetric chains. The H-bond Network Objective encourages players to bury H-bond Networks at the interface between the two chains. We've doubled the H-bond Network bonus, but we'd like players to focus on building networks deep in the core of the protein complex. There are a couple other bonuses in effect; see the puzzle comments for 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. The threshold of "buriedness" between core and surface residues is more stringent than usual, so residues may have to be "extra buried" to be counted toward the core.

Core Existence: Complex (max +3000)
Ensures that at least 60 residues are buried in the core of the entire complex (including the interface between monomer units).

HBond Network
Rewards networks that comprise at least three hydrogen bonds involving core residues. Networks must be at least 70% satisfied (i.e. 70% of all oxygens and polar hydrogens in a network must make a hydrogen bond).

SS Design (max +500)
Prohibits all CYS residues. Prohibits GLY, ALA residues in sheets and 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.

grogar7 Lv 1

Scoring engine is treating my entire symmetric chain as a non-ideal loop! That does not seem right!?

bkoep Staff Lv 1

You're right, that definitely shouldn't happen. Can you share this solution with scientists, and I'll take a closer look?