puzzle picture
1799: Sketchbook Symmetric Trimer Design: 90 Residues
Status: Closed


Name: 1799: Sketchbook Symmetric Trimer Design: 90 Residues
Status: Closed
Created: 02/13/2020
Points: 100
Expired: 02/20/2020 - 23:00
Difficulty: Intermediate
Description: This symmetric design puzzle has C3 symmetry, with three symmetric chains. This a Sketchbook puzzle with a Move Limit of 250 moves! After that, you will be unable to improve your solution, but you can restart the puzzle to reset your move count! The Move Limit is meant to encourage players to try lots of different folds, and we hope this will increase the diversity of player solutions. This puzzle is also 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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crowns's picture
User offline. Last seen 15 weeks 1 hour ago. Offline
Joined: 02/20/2020
Groups: None
How I played this puzzle

That's how I earned 10000 points:
1.Make all the chain into helix and then make it ideal.
2.Pull the chain into whatever shape.
3.Link the chain with its two mirrors and itself with as many rubber bands as possible in whatever ways and then wiggle to let the chain fold into a weird knot.
4.Click mutate and wait a few minutes.
5.Clear all the rubber bands and re-add rubber bands elsewhere, and repeat the steps above. Also try out "auto structures".
I'm new to this game. I don't know how such a random-generated protein will be used. If you have better ways please tell me.

Joined: 09/24/2012
Groups: Go Science
Find help or ideas from recipes

Great start but you should look at the bonusses: you 'll see there that your "monomer core" was not enough. In order to have a better core, cut your helix in 3-4 helices linked with loops of 1-3 and align the helices almost parallelly.

To do this, there are different ways: cut, align (closer and closer maximising the monomer core bonus), close the cuts. Or simply use the BluePrint tool. And/or freeze the helices, band them in order to fold them parallel, wiggle with Behaviour_Wiggle_Power 0.9 or 0.3 untill the Monomer Core bonus is ok.

When it's ok, freeze the all puzzle and continue with banding like you did or moving the 3 monomers together (with a look on the core complex: not too close). The remaining of your strategy is great.

You could have used the following recipe to be inspired for working designs:

When you are done with mutate, you could shake, wiggle sidechains, mutate again (all with wiggle power 1). Then unfreeze everything and wiggle with a look on your bonuses. If the bonuses are not ok, undo and try to stabilize more with mutate-shake and wiggle sidechains before to wiggle.

When you are done, try any banding recipe like GAB, Mutate Phobe Pull, banded worm pair etc. And/or AFK or Blue Fuse.

When you feel it's finished, think about turning wiggle power to High Wiggle Power and wiggle again.

LociOiling's picture
User offline. Last seen 9 hours 7 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
nice work, helixes rock

Helixes tend to score well, which is why design puzzles often limit how many segments can be in a helix.

You've discovered a variation of the Cynical Helix Ploy, where the rule is "when in doubt, make helixes".

Generally, three helixes parallel to each other is a good way to go. You'd generally use cutpoints and then the move tool to get them lined up. For some reason, four helixes tend to score lower than three, maybe because more segments are in the loops between helixes, where they don't score as well.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons