1855: Y1 Receptor ligand design

Closed since over 5 years ago

Summary

• Created: June 17, 2020
• Expires: July 01, 2020 at 23:00 UTC
• Max points: 100

Description

Use the new reaction design tool (blog post) to build a ligand which will bind well to the Y1 Receptor.



We've started you off with an arginine sidechain known to bind in the Y1 pocket. You can use the reaction design tool to grow this molecule to better fill the pocket. The molecules we're interested in at the moment are based on a central arginine core with "decorations" on either side. The reaction design tool will allow you to pick the best combination.



Since the precise 3D structure of the ligand is important, some of the reagent choices are very similar, except for the details of how the atoms are arranged (specifically, their chirality).



For more information about the Y1 receptor, see the previous puzzles: 1441, 1446, 1503 and 1653

Top groups

• 1. Gargleblasters 100 pts. 10,075
• 2. Go Science 73 pts. 10,061
• 3. Contenders 52 pts. 10,044
• 4. Anthropic Dreams 36 pts. 10,035
• 5. Void Crushers 24 pts. 10,015
• 6. Beta Folders 16 pts. 9,997
• 7. L'Alliance Francophone 10 pts. 9,969
• 8. Marvin's bunch 6 pts. 9,946
• 9. Russian team 4 pts. 9,896
• 10. Hold My Beer 2 pts. 9,842

Top soloists

• 1. donuts554 100 pts. 10,055
• 2. hpaege 98 pts. 10,051
• 3. mirp 95 pts. 10,045
• 4. CharlieFortsConscience 93 pts. 10,044
• 5. Skippysk8s 90 pts. 10,032
• 6. toshiue 88 pts. 10,025
• 7. Galaxie 85 pts. 10,024
• 8. Joanna_H 83 pts. 10,022
• 9. jeff101 80 pts. 10,020
• 10. NinjaGreg 78 pts. 10,011

Comments

[Formula350]

Is that we've been given this as a real-world Training Exercise.
The Tutorial level is to give you a quick and dirty "What this is, and how to use it" intro to Reaction Design. Granted, it's…. not very good at doing that right now, but that's besides the point lol

The point being that once you've been shown how the Tool functions, you need something to practice on and understand what and how you play the Ligand type of puzzles.
Again, there is a lot that we're not being given, information-wise, that would help us… but it is early and these sort of things continually receive polishing.

Beyond that, I would almost argue that having so few choices actually makes it ideal for us human meat-bags to be the ones to play it. If we had 30-choices in each column… can you IMAGINE how daunting that would come across? We'd need a month in order to figure out the best combo!
I would say then, that the Algo's tackle the giant list of candidates and refine it into a smaller one which "seem to work well". Then we get our fingers on them and work our magic to come up with creative ways to shoehorn that square peg into a round hole. :)

That's just my 2-cents though.

[jeff101]

Having LUA commands like at:

https://fold.it/portal/node/2009887

to pick the reactants and make the ligand would help.

[jeff101]

Since sharing solutions with Group doesn't seem to work for 1855
(Crashes 6-7 at https://fold.it/portal/node/2009873#comment-42080),
I'm guessing that sharing with Scientists won't work either.
With all the different ligand designs possible in Puzzle 1855,
this is a shame. I'd imagine there will be a great diversity
of solutions from each player. Because of this, I hope that
the Foldit Team will mine the many solutions automatically 
shared with the server as we play Puzzle 1855 online.

Perhaps posting a sequel to Puzzle 1855 after fixing all the
bugs with 1855 would help. It would also be nice if you would 
let us load solutions from Puzzle 1855 into this sequel puzzle.

Thanks!
Jeff

[LociOiling]

The wiki now has reaction design puzzle with a general description, and puzzle 1855 reaction design with more of a deep dive.

The big discovery for me was that the initial preview image does not match the initial selections when you open the reaction design panel.

When you open the panel, the top of each of the three columns is selected, so "1,1,1". But the preview shows you "4,4,2". If you actually click on those options, you'll notice the preview doesn't change.

I didn't figure all this out until about a week after the puzzle closed.