To say that the coronavirus has had a huge effect is to understate it. Aside from the health concerns, the impact has even affected economies. In the world of gaming, the effects have also started to creep in. Tournaments have been postponed, or even outright cancelled. Studios have also cancelled appearances to events and conventions.
However, if what Foldit is offering works, a solution against the coronavirus could be on the horizon.
Foldit is an online puzzle video game that was developed by the University of Washington. Using tools provided in the game, the goal is to fold the structures of selected proteins. The solutions that get the highest score are then analyzed by researchers to see if they can be applied to the real world. In effect, what Foldit offers is to crowdsource a possible solution to the current problem, which is the coronavirus.
The new puzzle is titled 1805b: Coronavirus Spike Protein Binder Design, with intermediate difficulty. The goal is to come up with a binder against the coronavirus.
As a background, the coronavirus is a highly-infections virus that came out of Wuhan, China in December of last year. The virus is seen by many as being similar to the one that caused the SARS epidemic way back in 2002. What the virus does is that it has a "spike" protein on their surface which then binds tightly to a receptor protein located on the surface of human cells. Once the virus manages to bind to the human receptor, it then infects the human cell and replicates. Recently, researchers have managed to determine the structure of the spike protein and how it actually manages to bind itself to human receptors.
For the new puzzle, players are given the binding site of the coronavirus spike protein. Most of the sidechains, along with the backbone, are completely frozen. The only exception to this is the sidechains that are the binding site. This is where the spike protein typically normally interacts with the human receptor protein.
Players are asked to come up with a new protein that binds to these sidechains, blocking interactions with the human receptor. To make sure that it does bind with the coronavirus target, the design has to have lots of contacts and H-bonds with the spike protein at this binding site. That's not all, as the designs also need to have lots of secondary structures plus a large core, to ensure that they fold up correctly.
Below are the actual objectives of the game:
- 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.
What are you waiting for? It's time to do your part.
