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1714: Symmetric Trimer Design: 100 Residues
Status: Closed


Name: 1714: Symmetric Trimer Design: 100 Residues
Status: Closed
Created: 08/14/2019
Points: 100
Expired: 08/21/2019 - 23:00
Difficulty: Intermediate
Description: This symmetric design puzzle has C3 symmetry, with three symmetric chains. This puzzle is a little different from other symmetry puzzles, in that we want players to focus on building a smaller interface between the chains. The "Core Limit: Complex" objective will incur penalties if there are too many buried residues in the total assembly. See the puzzle comments for Objective 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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bkoep's picture
User offline. Last seen 12 hours 43 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff

Core Existence: Monomer (max +3000)
Ensures that at least 30 residues are buried in the core of the monomer unit.

Core Limit: Complex (max +500)
Checks that no more than 105 residues are buried in the symmetric complex, including the interface between monomer units.

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA, SER, THR 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.

Joined: 09/20/2011
Groups: Marvin's bunch

This is ridiculous - I create a monomer with really good core.......the monomers are miles apart.

then the complex core filter penalises me. Surely this is not how this puzzle should work?

bkoep's picture
User offline. Last seen 12 hours 43 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
You're too good!

You're right! Ideally, the complex limit should only come into effect for residues that are buried at the complex interface—residues that are buried in the monomer unit should be exempt from the complex limit.

Unfortunately, the Core Limit Objective is not quite set up to handle this, and we thought it would be sufficient to impose the limit on the entire complex. We did not expect for players to so easily find solutions with so many residues in the monomer core. I apologize for the issue, although I am impressed by your design skills (I hope your solution was Shared with Scientists!).

The "Core Limit" puzzles are part of an ongoing experiment to see if it's helpful to limit the number of nonpolar residues at the symmetric interface. If the pilot analysis looks good, then we'll probably update Foldit to handle this situation better. In the meantime, we'll try to be a little more conservative with the Core Limit thresholds!

Joined: 09/20/2011
Groups: Marvin's bunch

the more I play this - the worse it gets.

My monomer should have no limit for core score - but it is seeping over and penalising even B4 I put the monomer near it's counterparts.

This puzzle should be denigrated - and the software sorted B4 being reposted

grogar7's picture
User offline. Last seen 11 hours 14 min ago. Offline
Joined: 10/03/2011
same problem as frood66

My monomer subunits are not in contact, but I'm getting Core Limit: Complex penalties. Was this really intended?

bkoep's picture
User offline. Last seen 12 hours 43 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Thanks for the feedback!

We apologize for the issue—we'll try to mitigate this in the future!

Please upload your solution using Share with Scientists! I'm very curious to see your design!

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