Design a protein to inhibit Coronavirus

FoldIt is software developed by arguably the world’s leading expert on proteins, David Baker at University of Washington. He has done pretty remarkable things that deserve more press than they get, such as designing novel protein folds in silico and then replicating them in nature. There’s no one alive that understands more about protein dynamics than he does.

Some years ago, he released a game called FoldIt. It’s a very simple game to play and requires no biological background, but instead relies on the intuition that humans innately have. Which is an interesting topic in and of itself, but basically, it involves folding proteins essentially by eye, and how quickly and well you do it generates a score. Somewhat sadly, this greatly outperforms most algorithms that attempt to do the same thing - this is one area where computers and AI simply can’t even come close to people in terms of understanding. (And there are some really interesting technical reasons for that I’d be happy to delve into if anyone is interested)

Currently, there is a push on FoldIt to develop a protein that can bind the Coronavirus spike protein. The coronavirus 19 spike protein sits on the outside of the capsid, we’ve seen images of it now thanks to Dr. Emmie de Witt at Rocky Mountain National Laboraties, who took the well publicized SEM micrographs of it. That spike protein interacts very tightly with some sort of protein on the human cell. We know that it must be similar to other coronavirus spike proteins, but different enough to cause a change in host (i.e. this now can target human cells).

If we can identify the specific interactions with the protein its targeting, that will go a long way towards antiviral therapies, as well as developing an efficient vaccine. The idea of FoldIt’s coronavirus game is to simply try to determine the type of fold that is responsible for binding covid-19’s spike protein.

I’d encourage everyone to give it a try - its actually rather fun.


FoldIt Status

Looks like FoldIt has had two active SARS-CoV-2/COVID-19 puzzles/challenges thus far:

I am curious if there will be a round 3; their latest blog post, announcing round 2, appears to be an interesting read.

Other forum mentions of folding-related work on SARS-CoV-2