1837: Coronavirus Binder Design: Round 9

Closed since almost 6 years ago

Summary

• Created: May 13, 2020
• Expires: May 20, 2020 at 23:00 UTC
• Max points: 100

Description

Design a binder against coronavirus! This puzzle introduces a new objective: the Buried Unsats Objective detects "unsatisfied" polar atoms that cannot make hydrogen bonds with the water surrounding the protein. If your designed protein creates Buried Unsats, then it will be less likely to fold and bind to the coronavirus target. (Note that this target protein includes 8 buried unsats that players will be unable to fix.) See the blog for more details about buried unsats, and for helpful tips to make a successful protein binder! Players will be unable to load solutions from previous puzzles.



In late 2019, a new highly-infections virus emerged out of Wuhan, China. This virus belongs to the coronavirus family, and is similar to the virus that caused the SARS epidemic in 2002. Coronaviruses display a "spike" protein on their surface, which binds tightly to a receptor protein found on the surface of human cells. Once the coronavirus spike binds to the human receptor, the virus can infect the human cell and replicate. In recent weeks, researchers have determined the structure of the 2019 coronavirus spike protein and how it binds to human receptors. If we can design a protein that binds to this coronavirus spike protein, it could be used to block the interaction with human cells and halt infection!



In this puzzle, players are presented with the binding site of the coronavirus spike protein. The backbone and most of the sidechains are completely frozen, except for flexible sidechains at the binding site, where the spike protein normally interacts with the human receptor protein. Players can design a new protein that binds to these sidechains, blocking interactions with the human receptor. In order to bind the coronavirus target, designs will need to make lots of hydrophobic contacts and H-bonds with the flexible sidechains at the binding site. But designs will also need to have lots of secondary structure (helices or sheets) and a large core, so that they fold up correctly! See the puzzle comments for Objective details.

Top groups

• 1. Go Science 100 pts. 15,383
• 2. Gargleblasters 83 pts. 15,373
• 3. Team India 68 pts. 15,266
• 4. Void Crushers 55 pts. 15,198
• 5. Contenders 44 pts. 15,197
• 6. Anthropic Dreams 35 pts. 15,195
• 7. Beta Folders 27 pts. 15,156
• 8. Marvin's bunch 21 pts. 15,017
• 9. L'Alliance Francophone 16 pts. 14,997
• 10. Penny-Arcade 12 pts. 14,970

Top soloists

• 11. Timo van der Laan 89 pts. 15,198
• 12. Galaxie 88 pts. 15,195
• 13. LociOiling 87 pts. 15,156
• 14. Bletchley Park 86 pts. 15,147
• 15. mirp 85 pts. 15,146
• 16. spvincent 84 pts. 15,138
• 17. clark92 83 pts. 15,130
• 18. Bruno Kestemont 82 pts. 15,124
• 19. Crossed Sticks 81 pts. 15,100
• 20. mathwins 80 pts. 15,087

Comments

[bkoep]

You can design disulfide bonds into your protein, and they might help stabilize your protein. But we do not think disulfides are necessary, and Foldit will not reward these with a score bonus.

[grogar7]

Thanks, bkoep, for your replies to my concerns above. Especially interesting are the Surface Area approximations and the implications for score when this filter is active.

[spdenne]

I just saved my 1843 solution from the main client with 10 BUNS, and loading it in the devprev client resulted in 13 BUNS, and a lower score.