1440: Aflatoxin Challenge: Round 1

Closed since over 5 years ago

Summary

• Created: October 13, 2017
• Expires: October 31, 2017 at 23:00 UTC
• Max points: 100

Description

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 first 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.



Note: Due to special interest in this puzzle, the deadline has been extended by one week, to October 31 at 23:00 UTC.

Top groups

• 1. Beta Folders 100 pts. 16,065
• 2. Gargleblasters 85 pts. 15,921
• 3. Go Science 72 pts. 15,899
• 4. Void Crushers 61 pts. 15,894
• 5. Anthropic Dreams 51 pts. 15,890
• 6. Contenders 42 pts. 15,850
• 7. Italiani Al Lavoro 35 pts. 15,759
• 8. Hun-Magyar Csapat 28 pts. 15,717
• 9. Marvin's bunch 23 pts. 15,677
• 10. Russian team 19 pts. 15,612

Top soloists

• 1. LociOiling 100 pts. 16,065
• 2. reefyrob 99 pts. 15,990
• 3. Timo van der Laan 97 pts. 15,894
• 4. Enzyme 95 pts. 15,875
• 5. eusair 93 pts. 15,860
• 6. spvincent 91 pts. 15,849
• 7. Mike Cassidy 90 pts. 15,842
• 8. Bruno Kestemont 88 pts. 15,825
• 9. johnmitch 86 pts. 15,816
• 10. retiredmichael 85 pts. 15,794

Comments

[toshiue]

smortier, per your request…connection issues discussed in IRC. Loaded 1440 approx. 0100 PST. Beginning around 0200 until bed (0600), various rhythmic connection issues. Diagnostics said it was neither me nor Comcast, but Comcast is infamous for late Sunday night undocumented meddlings. "Signature" of such is usually the rhythm pattern. Aside from dropped connections (very unusual here), variety of upload/download problems on shares, continuing into today. Top share on 1440 crashing regardless of client I try it on…unusual problems, not the usual garden variety we're familiar with. Sorry for not being more specific, problem's being especially vague (all the usual diagnostics /corrections/workarounds done, to not much avail). Thanks…

[NinjaGreg]

The loops tend to go crazy if I move one fairly radically, then wiggle. They stretch their cutpoints out really long, then zip back and go beyond, causing intersections with other SS, and my score goes to like -400000. Have to run a recipe to slowly work out the stresses before I can work on the moved loop. Adding bands just aggravates the loops, makes them go wilder. Make progress slow.

[Bletchley Park]

I would like to know if the sponsoring parties also agree to not patent the designs or derivatives and place them in the public domain ?

[Mike Cassidy]

A question on 1440, is it important to have as many bonds as possible on the ligrand? or just go for high score>

[Susume]

All findings from the Aflatoxin challenge puzzles will be in the public domain. This was promised in the challenge kick-off talks.

[Bletchley Park]

I would like to see a legally binding statement by the promotors (and affiliates) that they too will abide by the rule that all their findings and derivatives will be in the public domain.

[LociOiling]

As Susume says, this was in the materials we received ahead of the launch event.

It's easy to miss, but it's in the puzzle description. It's also in the Foldit aflatoxin blog post, at the end, right above the logos and the footnotes:

By participating in these Aflatoxin Challenge puzzles, 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.

This is a little different than paragraph g of the Terms and Conditions, which says the University of Washington decides ownership of results, including filing any patents. The T&Cs do say "[a]ll significant scientific discoveries […] made in game will be made publicly available". (Publicly available does not mean free for commercial use, as in the case of the LZW data compression technique, where the algorithm was published, but you had to pay a license fee to use it in a product.)

I like the idea of the aflatoxin results being "public domain", especially given the nature of the problem. To me, "public domain" means no licensing fees, as in the case of a literary work being public domain, but I am not the authority here. (I hope players don't start lawyering up.)

[Edit: clarified "public domain" appears in both puzzle description and blog post.]

[Bletchley Park]

Loci, Susume, The statement explicitly only mentions PLAYERS designs, NOT DERIVATIVE works from the SPONSORS. The fact that only players are so specifically mentioned casts the impression that it will be ok for sponsors to make patentable derivative works based on these (now free from claims !) 'players' designs.

These derivative works can then be turned into products and subsequently be sold to the very farmers we, the players, try to help. THAT patenting is what I explicitly would like to avoid, hence I will not participate in this project unless that is unambiguously clarified.

[LociOiling]

I agree that another sentence or two wouldn't hurt, but the term "public domain" is reasonably clear, and it appears in the blog post and the puzzle description. I did miss it the first couple of times I looked, could be a late edit, but I think I got hung up on the part about players not seeking their own IP protection for results. The Foldit Terms and Conditions (dated 8 March 2013) never allowed that anyway, as far as I can tell, giving the University of Washington the right to decide who owns what, results-wise.

One handout we received before the aflatoxin launch mentioned all results being in the public domain. The blog post is basically the same text as the handout, but adds the part about players not agreeing not to seek IP protection.

I added a comment to the blog post asking for a bit more clarity on the IP issue.

[LociOiling]

As I read the T&C, the U of W has always been free to exploit our results commercially as it sees fit. Having the results at least start life as public domain seems like a step forward.

Developing any results into something actually useful would likely require substantial further R&D. Maybe a foundation or government would fund something like that, maybe not. "Public domain" means that any non-profit or for-profit entity could develop derivative works. I'm not sure that the sponsors would be the most likely candidates for that R&D role, but I don't see a good reason to bar them from pursuing it while allowing the big agrichemical companies to jump in.

Personally, I willing to hazard a certain amount of time and effort without any more details. A detailed licensing statement would be nice, but it would require lawyers to interpret properly, and of course other lawyers could then dispute those interpretations. I would prefer to look on the new puzzles as a gift and play the game.