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1570: Symmetric Trimer Design: Hydrogen Bond Networks

Closed since over 7 years ago

Advanced Overall Design Symmetry

Summary

Created
September 03, 2018
Expires
Max points
100
Description

This symmetric design puzzle has C3 symmetry, with three symmetric chains. The H-bond Network Filter encourages players to bury satisfied H-bond networks at the interface between the three 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 a couple other filters 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: Ensures that at least 21 residues are buried in the core of the monomer unit.

Core Existence: Complex: Ensures that at least 72 residues are buried in the core of the entire complex (including the interface between monomer units). 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 of the protein complex.

HBond Network: Rewards networks that comprise at least three hydrogen bonds involving core residues. Networks must be at least 75% satisfied (i.e. 75% of all polar atoms in a network must make a hydrogen bond).

SS Design: Prohibits all CYS residues. Prohibits GLY, ALA residues in sheets and helices.

Bletchley Park Lv 1

It takes a solid 14 seconds to roll a helix, something that should be an instantaneous job. Other actions like freezing do not work as the system is too unresponsive. I have a current generation system.

LociOiling Lv 1

The max total filter bonus is +8070, broken down as:

Core Existence Monomer: +2260 max

Core Existence Complex: +3760 max

SS Design: +500 max

Hydrogen Bond Network: +1600 max

The h-bond bonus is 200 points per interface h-bond, up to a maximum of 8.

Thanks to reefyrob for sharing a solution with max bonus, makes determining this info pretty easy. He has 10 bonds in one network, but only six are interface bonds. The network bonds to one sidechain, then continues through a backbone oxygen atom to another sidechain.

DoctorSockrates Lv 1

I did this on my stream today, I just got too tired of waiting 3 seconds every time I chucked a building block into my monomer using Blueprint mode. I'm running an i7-7700K (4.20 GHz) with an SSD and graphics card setup, too. I just didn't have it in me to even finish a monomer.