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1900: Symmetric Trimer Design: H-bond Networks
Status: Closed


Name: 1900: Symmetric Trimer Design: H-bond Networks
Status: Closed
Created: 10/07/2020
Points: 100
Expired: 10/14/2020 - 23:00
Difficulty: Intermediate
Description: Design a symmetric protein trimer, with 3 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 1 day 54 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -150 points per atom (not including symmetric copies).

Core Existence: Monomer (max +2000)
Ensures that at least 20 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 +1800)
Rewards networks that comprise at least 3 H-bonds involving core residues.
Between 1 and 9 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.

Enzyme's picture
User offline. Last seen 52 years 5 weeks ago. Offline
Joined: 07/10/2008
Groups: None
2 Networks

After spending the last 2 puzzles trying to determine why I can't reach the max bonus for HBond Network, I think I finally found the issue. Only 1 network can contribute to the HBond Network score bonus.
"2 Networks" solution uploaded for Scientists if you wish to review it.

Joined: 03/28/2020
Groups: Go Science
Strange bonus behavior

Yes, I also found some strange behavior with the HBnet bonus. I had a design in which the HBnet which was actually larger than required for 1800 HBnet bonus. But granted bonus was LOWER than 1800. When I deleted a part of the net I got the full 1800 Bonus for this now smaller net. I don't think that this behavior is desired?!

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