2018: Symmetric D2 Tetramer Design: H-bond Networks

Closed since over 4 years ago

Summary

• Created: July 14, 2021
• Expires: July 21, 2021 at 23:00 UTC
• Max points: 100

Description

Design a D2 symmetric protein tetramer, with 4 identical chains of 90 residues each! Unlike the cyclical C4 symmetry that we are used to, the proteins in this puzzle will come together as a "dimer of dimers" with D2 symmetry. 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.

Top groups

• 1. Contenders 100 pts. 33,741
• 2. Anthropic Dreams 56 pts. 33,727
• 3. Beta Folders 29 pts. 33,498
• 4. Gargleblasters 14 pts. 31,488
• 5. Marvin's bunch 6 pts. 31,483
• 6. Go Science 2 pts. 31,271
• 7. Australia 1 pt. 28,799
• 8. L'Alliance Francophone 1 pt. 27,552
• 9. Void Crushers 1 pt. 27,317
• 10. SETI.Germany 1 pt. 0

Top soloists

• 81. antibot215 1 pt. 0
• 82. kyoota 1 pt. 0
• 83. brucederby 1 pt. 0
• 84. dahast.de 1 pt. 0
• 85. mkermani 1 pt. 0
• 86. uihcv 1 pt. 0

Comments

[bkoep]

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -200 points per atom (not including symmetric copies).

Core Existence: Monomer (max +2800)
Ensures that at least 28 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.

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

H-bond Network (max +2400)
Rewards networks that comprise at least 2 H-bonds involving core residues.
Between 1 and 12 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.

[Bruno Kestemont]

Due to repetitive crashes with new computer (see feedback crash crask crash), could you extend the deadline please ?

[bkoep]

Thanks for the crash reports, Bruno! Unfortunately, we are still not sure what causes these crashes, and our crash logs do not indicate that this puzzle affected worse than others. We will not extend the deadline for this puzzle.

[alcor29]

I now set my UNDO RAM at 5%, and have had no more crashing.

[Bruno Kestemont]

I had the same crash on an old computer, running random idealize. This recipe makes cuts and idealizes. This happens only on symmetric puzzles. I'll try with a simpler idealize recipe.

[milkshake]

Yes, we've developed a fix for the crash which is caused by setting RAM usage to a low value.

[milkshake]

I agree that there is a crash related to idealize or remix and that symmetric puzzles are especially crashy. If you come up with reliable steps to reproduce the crash, we would love to know. Those kind of reproduction steps help us a lot in tracking down crashes and fixing them.

[Skippysk8s]

mine seemed to crash with anything using the mutate function
I wasn't able to spend much time on it, and was only trying to evo a hand fold. Quite frustrating