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1947: Symmetric Tetramer Design: H-bond Networks
Status: Closed


Name: 1947: Symmetric Tetramer Design: H-bond Networks
Status: Closed
Created: 01/21/2021
Points: 100
Expired: 01/29/2021 - 23:00
Difficulty: Intermediate
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.
Categories: Design, Overall, Symmetry

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bkoep's picture
User offline. Last seen 5 hours 31 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff

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.

LociOiling's picture
User offline. Last seen 5 hours 4 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders

Looks more like a tetramer to me.

bkoep's picture
User offline. Last seen 5 hours 31 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
You're right!

I've corrected the puzzle title now to read 'tetramer' instead of 'trimer'

Joined: 03/28/2020
Groups: Go Science
Frequent crashes

Is it just for me or does someone else also have the problem that Foldit crashes very often especially with this puzzle? This problem seems to be worse the more residues there are. Seems like this is triggered by recipes when they do a (global) wiggle and achieve a point gain. "Deep Remix Wiggle" likes to do this very often.

bkoep's picture
User offline. Last seen 5 hours 31 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Thanks for the feedback

This is the first we've heard about problems with the puzzle. You say it seems related to residue number; have you noticed similar crashes on other symmetry puzzles? On other non-symmetry puzzles?

If you're able to find a 100% reliable way to produce the crash, please share details with us! Or share your solution with the Upload for Scientists button. That would be immensely helpful for tracking and fixing the bug.

Joined: 03/28/2020
Groups: Go Science
It's a general problem

I have seen this on other puzzles as well. For example on 1945 where also quite many residues are present. I have no problem with the prediction puzzles like 1946 (which has no filters). Ran overnight with 8 clients in parallel and no crash. With this puzzle I typically get a crash after a few minutes especially with "deep remix wiggle". I think it is related to some filter since I always have all filters on while running recipes. Also I have in most cases multiple clients running in parallel with different recipes. But I don't think this is a problem since I saw these crashes also on a single client running just basic wiggle-operation (called from recipe). To reproduce just run "deep remix wiggle" with all filters active and it should crash quite soon. I can send more info on which version of it I am using and my current solution. I can also send my options.txt so that you know how my clients are configured. Thanks in advance!

grogar7's picture
User offline. Last seen 12 hours 13 min ago. Offline
Joined: 10/03/2011
crashing on puzzle 1947

I, too, have had trouble with crashing on this puzzle. Some recipes produce crashing reliably, notably Tvdl DRemixW, Tvdl Mutate Combo, and Simulated Annealing 5.0. I am not certain which operations within those recipes are producing crashes. I have Shared with Scientists and placed notes in the Share Description regarding recipes that are crashing.

The share is titled 'puzzles crashes'

Joined: 06/06/2013
Groups: Gargleblasters
symmetry puzzles seem the worst

I gave up on the last tetramer. Despite having a decent gaming computer it kept crashing. I had a lot of trouble with anything that mutated the protein -- dremix, mutate by layers, bandfuse. I never got to the point of trying to find h bonds as I could not get a basic fold to stay up long enough to get past all filters

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