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1850: Symmetric Trimer Design: Buried Unsats

Closed since over 5 years ago

Intermediate Overall Design Symmetry

Summary

Created
June 11, 2020
Expires
Max points
100
Description

Symmetric puzzles are back! Design a symmetric protein trimer, with 3 identical chains that assemble together. This puzzle uses the new Buried Unsats Objective but this objective will not award any points. The H-bond Network Objective encourages players to bury 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! 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 +0)
Detects polar atoms that cannot make hydrogen bonds. This Objective awards no bonus or penalty.

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 two 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).

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.

Skippysk8s Lv 1

For some reason, I am unable to play this puzzle. It has crashed running dremix. it has crashed running bandfuze. it will not stay up

I love symmetry puzzle and am totally bummed out.

grogar7 Lv 1

I, too, am crashing with Timo van der Laan's DRemixW 3.1.2. This may be an issue with that particular script. Has anyone found a remix script that is stable with this puzzle?

Serca Lv 1

Skippysk8s, grogar7

If that is the issue of that particular script, you might try to run my remix script instead of Tvdl's one.
https://fold.it/portal/recipe/103403

It's not the real DRemixW script but it can be used for overnight full protein remix.
You need to select 3 checkboxes in the options for that:

  • Remix instead of rebuild
  • Full protein Rebuild
  • Infinite execution

BootsMcGraw Lv 1

How does one get the monomers to stay close enough to make H-bonds with each other? Putting them close together causes the score to drop below zero and the monomers to explode upon wiggle. Putting them at a distance that gives a positive score causes the wiggle function to just push the monomers further apart.