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2018: Symmetric D2 Tetramer Design: H-bond Networks
Status: Closed

Summary

Name: 2018: Symmetric D2 Tetramer Design: H-bond Networks
Status: Closed
Created: 07/14/2021
Points: 100
Expired: 07/21/2021 - 23:00
Difficulty: Intermediate
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.
Categories: Design, Overall, Symmetry

Top Groups

RankGroupScorePoints
1Contenders33,740100
2Anthropic Dreams33,72656
3Beta Folders33,49829
4Gargleblasters31,48714
5Marvin's bunch31,4836

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Top Soloists

RankPlayerGroupScorePoints
1alcor29 5 13 Anthropic Dreams33,642100
2LociOiling 4 1 Beta Folders33,49895
3CharlieFortsCon... 34 58 Contenders33,40989
4sgeldhof 70 12  32,37684
5dcrwheeler 70 5  31,79279


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Comments

bkoep's picture
User offline. Last seen 2 days 8 hours 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 +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.

Joined: 09/24/2012
Groups: Go Science
Extend the deadline

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

bkoep's picture
User offline. Last seen 2 days 8 hours ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
No extension

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.

Joined: 09/24/2012
Groups: Go Science
something related to idealize or remix

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's picture
User offline. Last seen 2 weeks 4 days ago. Offline
Joined: 07/17/2019
Groups: Foldit Staff
I agree that there is a crash

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.

alcor29's picture
User offline. Last seen 14 hours 4 min ago. Offline
Joined: 11/16/2012
RAM Fix?

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

milkshake's picture
User offline. Last seen 2 weeks 4 days ago. Offline
Joined: 07/17/2019
Groups: Foldit Staff
Yes, we've developed a fix

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

Joined: 06/06/2013
Groups: Gargleblasters
mine kept crashing too

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

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