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1619b: Symmetric Trimer Design: Hydrogen Bond Networks
Status: Closed

Summary

Name: 1619b: Symmetric Trimer Design: Hydrogen Bond Networks
Status: Closed
Created: 01/05/2019
Points: 100
Expired: 01/11/2019 - 23:00
Difficulty: Advanced
Description: This symmetric design puzzle has C3 symmetry, with three symmetric chains. The H-bond Network Objective encourages players to bury H-bond Networks at the interface between the two chains. We've doubled the H-bond Network bonus, but we'd like players to focus on building networks deep in the core of the protein complex. There are a couple other bonuses in effect; see the puzzle comments for details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!
Categories: Design, Overall, Symmetry

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RankGroupScorePoints
1Contenders27,660100
2Russian team26,88976
3Gargleblasters26,88356
4Anthropic Dreams26,45841
5Go Science26,44629

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Comments

bkoep's picture
User offline. Last seen 17 hours 50 min ago. Offline
Joined: 11/15/2012
Groups: None
Objectives

Core Existence: Monomer (max +3000)
Ensures that at least 21 residues are buried in the core of the monomer unit. The threshold of "buriedness" between core and surface residues is more stringent than usual, so residues may have to be "extra buried" to be counted toward the core.

Core Existence: Complex (max +4650)
Ensures that at least 72 residues are buried in the core of the entire complex (including the interface between monomer units).

HBond Network
Rewards networks that comprise at least three hydrogen bonds involving core residues. Networks must be at least 70% satisfied (i.e. 70% of all oxygens and polar hydrogens in a network must make a hydrogen bond).

SS Design (max +500)
Prohibits all CYS residues. Prohibits GLY, ALA residues in sheets and 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: 06/24/2008
Groups: Void Crushers
Score

How many extra pmts can you get on the two core Exustences? I am already above the score that is given.

bkoep's picture
User offline. Last seen 17 hours 50 min ago. Offline
Joined: 11/15/2012
Groups: None
Strange

Can you share your solution with scientists? There may be a bug, and that should help us track it down.

The puzzle configuration is definitely set to max out at +3000/+4650 pts for the Monomer/Complex objectives.

Joined: 03/05/2015
Groups: Gargleblasters
We have no blueprint tool / Rama map for this puzzle?

Intentional or oversight? I don't see either in the tools.

bkoep's picture
User offline. Last seen 17 hours 50 min ago. Offline
Joined: 11/15/2012
Groups: None
Should be available

This is also odd. Both the Rama Map and Blueprint Tool should be available, and I can use them just fine here. Are other people also seeing this issue?

Joined: 11/09/2018
Groups: None
Core existence

Monomer max +3050
Complex max +4700

bkoep's picture
User offline. Last seen 17 hours 50 min ago. Offline
Joined: 11/15/2012
Groups: None
Share with scientists

Can you share your solution with scientists? This seems like a bug; those objectives should max out at +3000 and +4650.

dbuske's picture
User is online Online
Joined: 09/22/2011
Groups: Beta Folders
Problems

These puzzles have a problem.
They don't seems to allow 360 degree rotation.
They are very madding to work on.

jeff101's picture
User offline. Last seen 21 min 42 sec ago. Offline
Joined: 04/20/2012
Groups: Go Science
Some tricks for symmetry puzzles:

Hopefully some of the comments below for symmetry
puzzles 1499 and 1499c will help with this puzzle:
https://fold.it/portal/node/2004908#comment-36407
https://fold.it/portal/node/2004919#comment-36442

bkoep's picture
User offline. Last seen 17 hours 50 min ago. Offline
Joined: 11/15/2012
Groups: None
Details?

Can you say more about the rotation problem?

Do you mean you're having trouble rotating the camera (by clicking and dragging the background)? Or are you having trouble rotating the protein (using the move tool)?

Does the client crash, or do the tools stop working while Foldit continues to run?

jeff101's picture
User offline. Last seen 21 min 42 sec ago. Offline
Joined: 04/20/2012
Groups: Go Science
Puzzle 1619b is very slow
I'm not sure what rotation problem dbuske was describing 
above. It might be similar to what I experienced in Puzzles 
1499 & 1499c. It might be like what Skippysk8s encountered 
last March (https://fold.it/portal/node/2004913), perhaps 
also for Puzzles 1499 & 1499c.

My own experience with Puzzle 1619b is that it is very slow.
Even simple things like Restore Recent Best, scrolling thru 
Chat, and Freeze/Unfreeze have been much slower than usual. 
I got a Recipe to evo a teammate's solution at least. This 
Recipe also ran much slower than usual. I'll probably not 
try to solo on this puzzle.

I did glance at the Rama Map & Blueprint Tool in the 
Original Interface when I started this puzzle. They looked 
normal. I was also able to rotate two of my teammates' 
solutions around to see which residues were already involved 
in hydrogen bond networks. Things behaved fine in my hands, 
but I think all the clients I used were old ones, like from 
September 2018.
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