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1888: Symmetric Trimer Design: H-bond Networks

Closed since over 5 years ago

Intermediate Overall Design Symmetry

Summary

Created
September 09, 2020
Expires
Max points
100
Description

Design a symmetric protein trimer, with 3 identical chains that assemble together! Note the Interaction Energy Objective, which will penalize poorly-scoring large residues that can lead to unwanted protein aggregation. The H-bond Network Objective encourages players to build buried, satisfied H-bond networks at the interface between symmetric chains. H-bond networks are a great way to introduce polar residues at the interface, but it's important that all of the bondable atoms make hydrogen bonds! We've also adjusted the H-bond Network Objective so that poor-scoring H-bonds may not contribute to networks; poor-scoring H-bonds will be displayed in red. This puzzle uses the Buried Unsats Objective, with a large penalty for buried polar atoms that can't make H-bonds. In this puzzle, there are no limits on the Complex Core, but we've included the Complex Core objective so players can see the core residues that can be incorporated into H-bond Networks.

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Comments

bkoep Staff Lv 1

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -150 points per atom (not including symmetric copies).

Core Existence: Monomer (max +2000)
Ensures that at least 20 residues are buried in the core of the monomer unit.

Core: Complex (max +0)
Awards no bonuses or penalties. Click Show to see which residues count as "Core" for the H-bond Network objective.

H-bond Network (max +1800)
Rewards networks that comprise at least 3 H-bonds involving core residues.
Between 1 and 9 H-bonds should cross the interface between symmetric units.
Networks must be at least 75% satisfied (i.e. 75% of all bondable atoms in a network must make a H-bond).

Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.

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

CharlieFortsConscience Lv 1

This one seems a little erratic, specifically the Unsats filter. I'm doing my usual start games moves, setting my structure and mutating. When I wiggle it out, I'm getting a lot of high 'ghost scores', where the score reaches high, then settles a lot lower, many hundreds of points lower, when wiggle has run its course, seems to be the Unsats filter doing it.

Also, mutating at lower clash levels seems to give odd poses with some oddly enriched sidechains - please see the 17337 score I uploaded to scientists. I'd expect more TRPs n PHEs at .08 clash.

This one just doesnt feel like a horse that wants to ride on the right side of the road.

bkoep Staff Lv 1

The TRP and PHE changes are expected, and result from the Interaction Energy Objective. We're a little worried about excessive amounts of TRP and PHE in recent designs, and the objective is intended to limit those amino acids.

Otherwise, this puzzle is nearly identical to the recent symmetric puzzles. The Buried Unsats Objective could be pretty erratic during early game if you are working with a partially folded structure. I might recommend disabling that Objective until you have a well-folded backbone.

The "ghost scores" phenomenon is strange; if you're able to reproduce the issue, please Share with Scientists!