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1595: Aflatoxin Challenge: Round 12
Status: Closed

Summary

Name: 1595: Aflatoxin Challenge: Round 12
Status: Closed
Created: 11/02/2018
Points: 0
Expired: 11/09/2018 - 23:00
Difficulty: Intermediate
Description: Note: Due to a bug in solution sharing and loading, this puzzle is worth zero points and will close early. We encourage players to play replacement puzzle Puzzle 1597 instead, although we will still analyze the solutions from this puzzle if players wish to keep working on their designs. Unfortunately players may not load solutions from this puzzle into the replacement Puzzle 1597.

Redesign the active site to bind aflatoxin! This is Round 12 of the Aflatoxin Challenge. This puzzle is much like the previous round, with some active site mutations from the Siegel Lab, and players may load solutions from Round 11 into this puzzle. However, players have some more freedom in this puzzle to redesign three loops around the active site where aflatoxin binds. Players may insert up to 20 extra residues into these designable loops, at a cost of 20 points per residue. Parts of the scaffold protein have been trimmed to reduce the size of the puzzle, and we've upweighted ligand interactions by a factor of five. We'd like to see if Foldit players can design proteins that make more interactions with the ligand! See the blog for more details.

Aflatoxins are a class of poisonous compounds that contaminate a significant portion of the global food supply. In this puzzle, players are challenged to redesign an enzyme that could break down aflatoxin molecules. The majority of the protein is frozen, with the aflatoxin ligand fixed in a binding pocket. Surrounding the binding pocket are a number of loops that might be redesigned without affecting the folding stability of the protein. In these loops, players may manipulate the protein backbone and mutate the residue sidechains. Redesign the loops of this protein to better bind the aflatoxin ligand!

This is the twelfth puzzle of our Aflatoxin Challenge, sponsored by Mars Inc. and Thermo Fisher Scientific. Promising designs will be tested by the Siegel Lab at UC Davis. By participating in the challenge/game, the players agree that all player designs will be available permanently in the public domain, and the players will not seek intellectual property protection over the designs created as part of the challenge/game.
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1Contenders13,2820
2Go Science13,1450
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5Beta Folders13,0850

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Comments

Joined: 05/21/2010
Groups: Go Science
Appreciate the new puzzle, but ...

... the fixed part of the protein isn't fixed. The part between the loops we could modify before, and the new one we could modify (the one fastened at both ends), came loose when I was pulling on the latter loop. Probably not what you intended.

Joined: 05/21/2010
Groups: Go Science
Segs 46-65

Guess I could have determined that before posting the prior comment.

bkoep's picture
User offline. Last seen 6 hours 36 min ago. Offline
Joined: 11/15/2012
Groups: None
Shared solution?

Hm, I'm having trouble reproducing this. Can you share your solution with scientists?

The three designable loops are not locked in place at all. You should have complete freedom to move them around and even separate them from the protein (but the should score poorly if you extend the cutpoints).

However, that range of residues (46-65) should be completely fixed. (Note that, if any residues have been inserted into your solution then the numbering will be off. It will be easier for us to debug the shared solutions.)

Mark-'s picture
User offline. Last seen 2 days 12 hours ago. Offline
Joined: 08/05/2009
Groups: Contenders
Shared solutions

I can get my 44-63 residues to move by idealizing residues 27-43. They appear to return from where they came from but have uploaded my current solution for someone to check out as I did make a nice score gain around that time.

Uploaded two solutions one is my current high score and the other is after idealizing res. 27-43.

Happy to answer any further questions

bkoep's picture
User offline. Last seen 6 hours 36 min ago. Offline
Joined: 11/15/2012
Groups: None
Replacement puzzle

Thanks for the feedback, all! It seems that some of these problems (see here) were related to solution sharing. When you encountered this bug, were you working with a solution that was shared from the previous aflatoxin round (Puzzle 1590b)?

We've closed this puzzle and reposted it with sharing disabled, as Puzzle 1597: Aflatoxin Challenge: Round 12b. If you continue to encounter these problems in the new puzzle, please let us know!

spvincent's picture
User offline. Last seen 46 min 39 sec ago. Offline
Joined: 12/07/2007
Groups: Contenders
Aflatoxin/FoldIt in Nature

Mars has put up a sponsored feature on this in a recent edition of Nature (one with a picture of a cuttlefish on the front cover).

It's online at https://www.nature.com/articles/d42473-018-00170-5

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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