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2050: Symmetric D2 Tetramer Design with AlphaFold Predictions
Status: Closed

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bkoep's picture
User offline. Last seen 8 hours 42 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -200 points per atom (not including symmetric copies).

Core Existence: Monomer (max +1600)
Ensures that at least 16 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.

Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.

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).

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.

alcor29's picture
User offline. Last seen 7 hours 56 min ago. Offline
Joined: 11/16/2012
missing penalty

Description say use no more thatn 50% helices but there is no penalty in the filter menu.

bkoep's picture
User offline. Last seen 8 hours 42 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Good catch!

That was an error in the puzzle description; this puzzle should permit as much alpha helix as you want! I've corrected the puzzle description.

HuubR's picture
User offline. Last seen 7 hours 50 min ago. Offline
Joined: 04/13/2020
Groups: Gargleblasters
Bands STILL do not work as intended!

My initial reaction was:  Wow, another D2 Symmetry puzzle.  Nice!

But then I thought, before I spend a lot of work on a new design, let me have a look at the way bands between the chains work now. As I pointed out in a feedback item last June, this was a bug in the previous D2 symmetry puzzles.

This quick test was a bitter disappointment:  the bug has not been resolved.   :-(

I would like to hear from Foldit Staff what has been done in the past three and a half months to address this (as milkshake announced in this comment), and also: when can we expect a fix?

For now, all we can do is avoid any bands to chain 1 (purple) and chain 3 (brown), or, if you need a band to one of these chains, use this workaround.

bkoep's picture
User offline. Last seen 8 hours 42 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Hmm

I had thought this bug was fixed when we addressed the HBNetwork issues with D2 symmetry. We'll have to dig back into it, but it looks like a potentially hairy bug, so may be difficult to track down.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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