1989: Symmetric Tetramer Design: H-bond Networks

Closed since almost 5 years ago

Summary

• Created: May 05, 2021
• Expires: May 12, 2021 at 23:00 UTC
• Max points: 100

Description

Design a symmetric protein tetramer, with 4 identical chains that assemble together! This puzzle includes a Secondary Structure Objective, so no more than 50% of your design can form helices. 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. 24,563
• 2. Go Science 70 pts. 24,324
• 3. Beta Folders 47 pts. 23,609
• 4. Marvin's bunch 30 pts. 21,980
• 5. Anthropic Dreams 19 pts. 21,807
• 6. Void Crushers 11 pts. 21,429
• 7. Gargleblasters 7 pts. 20,433
• 8. Australia 4 pts. 18,746
• 9. L'Alliance Francophone 2 pts. 16,034
• 10. BOINC@Poland 1 pt. 15,895

Top soloists

• 1. ichwilldiesennamen 100 pts. 24,267
• 2. spvincent 96 pts. 24,046
• 3. silent gene 91 pts. 23,982
• 4. LociOiling 87 pts. 23,609
• 5. Bruno Kestemont 83 pts. 23,193
• 6. fiendish_ghoul 79 pts. 23,133
• 7. mirp 75 pts. 22,339
• 8. frood66 71 pts. 21,980
• 9. martinzblavy 68 pts. 21,871
• 10. dcrwheeler 64 pts. 21,857

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.

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).

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.

Secondary Structure (max +500)
No more than 50% of residues may form helices. Extra helices are penalized at 10 points per residue.

[Mike Cassidy]

This puzzle has crashed twice on me.

[milkshake]

Hi Mike Cassidy, what action are you performing when it crashes? Running a script, making a band, mutating a residue, etc.? If you're doing something manually, is a script running at the same time? Thank you.

[blazegeek]

This puzzle crashes on me at random, regardless of what I am doing. Manually wiggling, shaking, mutating, and idealizing have all crashed the puzzle repeatedly. I don't think I've had an opportunity to even run any scripts yet.

[grogar7]

Just to throw in my 2 cents worth, this puzzle is repeatedly crashing for me, too! Cause does not seem to be consistent. For example, Tvdl DRemixW will invariably crash, but sometimes it is immediately after selecting options and starting puzzle run and other times it will run through several sets of segments before crashing. Same problem with GAB_proj_beta. Has also occurred with some manual actions.

Interestingly, Maaa version 2.4.2 did not crash!

Very frustrating, especially as I suspect the problem will not be reproducible by our scientists.

[BootsMcGraw]

Every time I try to run a mutate script or a rebuild on this puzzle, it crashes within fifteen minutes.

Unplayable. Please cancel this puzzle and replace it with one that works.

[milkshake]

This type of crash may be somewhat difficult to reproduce and to track down, but we have ideas about what may be causing them and myself and other developers are working on the problem. We believe that low framerates, high residue count, and possibly interactions in our molecular modeling layer that are unaccounted in our graphics layer may contribute to the problem. We'll stay in communication and post patch notes when we do figure things out. I've fixed at least one crash so far related to this puzzle/caused by low frame rate, but there may be several in the same vein.

[alcor29]

At lest 14 crashes. Main. Win10 64. Both solo and evo. Had to abandon.

[milkshake]

Drawing bands while wiggling was the cause of the crash that has already been fixed, and will be pushed to the main client soon.

For another long-running script crash, it might help to use View Protein: Cartoon, View Hydrogens: Hide All H, and View Sidechains: Don't Show (Fast). This is a workaround and we are working on a long-term fix.

[HuubR]

Tried all sorts of diffrent view settings, LWP, MWP, high CI, low CI, but nothing seemed to help. Just found out in the last half hour before closing that switching off the Hydrogen Bond Network filter does help, at least for two very persistent crahes (in two different tracks) that I had.
For what it is worth: 20210429-924409cca5-win_x86-devprev