puzzle picture
1808: Coronavirus Binder Design: Round 2
Status: Closed


Name: 1808: Coronavirus Binder Design: Round 2
Status: Closed
Created: 03/05/2020
Points: 100
Expired: 03/12/2020 - 23:00
Difficulty: Intermediate
Description: Design a binder against coronavirus! This is a followup to Puzzle 1805b, which challenged players to design an antiviral protein that could bind to the 2019 coronavirus and disrupt viral infection. This puzzle has some small improvements, and allows players to continue working on antiviral designs. See the Foldit blog for a quick look results from Puzzle 1805b, with some tips for making a successful protein binder! Players may load in solutions that were saved in the previous puzzle.

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.
Categories: Design, Overall

Top Groups

2Go Science15,83283
4Anthropic Dreams15,82056
5Beta Folders15,79245

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Joined: 09/24/2012
Groups: Go Science
Same objectives as before

Residue Count (max +550)
Penalizes extra residues inserted beyond the starting 192, at a cost of 55 points per residue. Players may use up to 202 residues in total.

Core Existence (max +2400)
Ensures that at least 28 percent of residues are buried in the core of the monomer unit.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.

The total maximum bonus is 3950

LociOiling's picture
User offline. Last seen 1 hour 34 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
typo patrol

The line:

a new highly-infections virus

should read:

a new, highly infectious virus

I considered a second comma in there, but decided against it.

Joined: 03/04/2020
Groups: None
hello im an artist and I understand hlab27 gene has some immunit

is that your covirus protein? you have lots of sheets !
so the new challenge is to design a protien that will bind to the human site ?

Joined: 09/24/2012
Groups: Go Science

The challenge is to design a protein that will bond to the virus site (so that it cannot bind to the human site)

LociOiling's picture
User offline. Last seen 1 hour 34 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
evolver play a problem

This puzzle lets you continue work on your 1805b results, but evolver mode is a problem, since solutions load with much lower score, but evolving them still requires adding two points to the 1850b score.

For example, my 1805b solution scoring 16,534 loaded at 15,704 in 1808. But it still wants 16,536 to evo. I saw similar results in other solutions. I'm guessing that most of the evolvers are working on new solutions.

Joined: 03/11/2020
Groups: None
We Must Solve this CoronaVirus

This Coronavirus is a killer. I send my prayers to the families of the dead to this horrible disease. If one of us could crack this case, lives would be saved. As a society we must solve this. Please help everyone this needs to be solved. Nobody else should die.

jeff101's picture
User offline. Last seen 14 hours 28 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Can players load Beginner Coronavirus Puzzle solutions here?

Can players load their solutions
from the Beginner Coronavirus Puzzle
into this one?

bkoep's picture
User offline. Last seen 1 day 52 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
No loading from Beginner Puzzle

No, solutions from the Beginner puzzle are incompatible with this puzzle. Players may not load solutions from the Beginner puzzle.

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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, Boehringer Ingelheim, RosettaCommons