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1894: Symmetric Trimer Design: H-bond Networks
Status: Closed


Name: 1894: Symmetric Trimer Design: H-bond Networks
Status: Closed
Created: 09/23/2020
Points: 100
Expired: 09/30/2020 - 23:00
Difficulty: Intermediate
Description: Design a symmetric protein trimer, with 3 identical chains that assemble together! Note the Interaction Energy Objective, which will penalize poorly-scoring large residues that can lead to unwanted protein aggregation. 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 3 hours 33 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 +2200)
Ensures that at least 22 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 2 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).

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: 09/29/2016
Groups: Gargleblasters
It's late and you deserve rest, too!

So I won't ping you over Discord :P
However, we're all getting an error, even with the latest update:

downloading: http://fold.it/portal/files/puzzle_pdb/puzzle_post_2053.zip
has key .ocmdline
has key .sym
has key .roscript
has key .owts
Exception: Both weights file and score function name supplied. in ..\..\..\source\src\standalone\application\boinc\Puzzle.cc line 1403

bkoep's picture
User offline. Last seen 3 hours 33 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff

Thanks! Should be fixed.

Also, the September 23 update is required to open this puzzle.

spvincent's picture
User offline. Last seen 14 hours 25 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Since the changes to H-Bond

Since the changes to H-Bond Network scoring a few puzzles ago, which were largely aimed at preventing serine triangles and similar constructs, I've found it a lot harder to create networks of any kind. If this means that the new version reflects reality better than so be it, but I can't help wondering if the changes may have been too restrictive.

bkoep's picture
User offline. Last seen 3 hours 33 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Better networks

It's hard to make blanket conclusions about all H-bond networks. But we have definitely noticed a general improvement in the quality of H-bond networks since those changes -- especially in the top-ranking solutions.

Before, it was not unusual for us to find a few "unrealistic" H-bond networks (usually with subtle problems in H-bond geometry) among the top-scoring solutions from a puzzle. It seemed these networks were being awarded a big bonus that did not represent a true improvement in design quality.

It makes sense that it's harder to create networks with the recent changes. But it appears that the new HBNet Objective is in fact better about awarding bonuses that reflect real improvements in solutions. (At least, the solutions look better to Foldit scientists; we won't really know about any improvements until we get to test the designs in the lab).

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