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2012: Symmetric D2 Tetramer Design: H-bond Networks
Status: Closed

Summary

Name: 2012: Symmetric D2 Tetramer Design: H-bond Networks
Status: Closed
Created: 06/30/2021
Points: 100
Expired: 07/07/2021 - 23:00
Difficulty: Intermediate
Description: Design a D2 symmetric protein tetramer, with 4 identical chains of 80 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.
Categories: Design, Overall, Symmetry

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Comments

bkoep's picture
User offline. Last seen 12 hours 10 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

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

Core Existence: Monomer (max +2200)
Ensures that at least 22 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.

spvincent's picture
User offline. Last seen 8 hours 38 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Import

It would be nice if we could import monomers from previous puzzles.

alcor29's picture
User offline. Last seen 12 hours 25 min ago. Offline
Joined: 11/16/2012
Crashy

I have now crashed 29 times on 2012. I don't feel like I am designing proteins so much as fighting foldit. And now I can't blame my machine.
It's been a long time and there doesn't seem to be any progress. Very discouraging folks.

Joined: 03/28/2020
Groups: Go Science
Did you try this?

Have you tried the workaround in https://fold.it/portal/node/2011479? The reduction of the graph-length works for me to stabilize things.
The more residues there are in the puzzle, the more crashy things get. At least that is what I noted.

alcor29's picture
User offline. Last seen 12 hours 25 min ago. Offline
Joined: 11/16/2012
Thanks

Thanks ichwilldiesennamen. I have tried other undo setups, but I will try 25/20.

alcor29's picture
User offline. Last seen 12 hours 25 min ago. Offline
Joined: 11/16/2012
Thanks again

It seems to be working. Mutate combo is actually running. If It crashes later I will try even lower RAM.

alcor29's picture
User offline. Last seen 12 hours 25 min ago. Offline
Joined: 11/16/2012
More....

OK It crashed on 20% and 10% RAM. Doing OK on 5% RAM so far......

Joined: 03/28/2020
Groups: Go Science
Matches with what I see

I have long-running clients that I let run with graph-length 25 and RAM 0%. These run stable except for when I am running "Deep Remix Wiggle" which crashes reliably after a few minutes :(
On clients that I use for designing I use 25/100% so that I can flip back in the undo-history.
This works sufficiently well for me. When I run long-running recipes on the design-clients (with 25/100%) then I do get crashes after a couple of hours typically. This is not nice but acceptable.
So this matches pretty well with the values you stated.

All in all it seems to me like Foldit has problems with memory-management (or rather undo-data treatment). I often get crashes when multiple sets are loaded from quicksave-slots into undo-stack after a recipe has run for a long time (similar to what HNetwork Probe does). That seems to suicide Foldit with high reliability :)

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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