Survivalism & Self Sufficiency Topics > COVID-19 Coronavirus Pandemic

Ways to help with COVID-19 research while you're stuck at home


Mr. Bill:
Protein folding is a vital part of research into many aspects of biology including COVID-19.  You, or even your kids, can help with this, by playing a protein-folding computer game called Foldit.

The Science Behind Foldit

--- Quote ---Foldit is a revolutionary crowdsourcing computer game enabling you to contribute to important scientific research. This page describes the science behind Foldit and how your playing can help.
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Frequently Asked Questions

--- Quote ---What are the Rules of Foldit?

Here are the basic principles to keep in mind when folding proteins. Your score on each protein is based on how well you do with these three things.

1. Pack the protein
The smaller the protein, the better. More precisely, you want to avoid empty spaces (voids) in the structure of the protein where water molecules can get inside. So you want the atoms in the protein to be as close together as possible. Certain structures, such as sheets, will even connect together with hydrogen bonds if you line them up right and get them close together. This is also good. Key word: Compact.

2. Hide the hydrophobics
Hydrophobics are the sidechains that don't want to be touching water, just like oil or wax. Since most proteins float around in water, you want to keep the hydrophobics (orange sidechains) surrounded by as many atoms as possible so the water won't get to them. The other side of this rule is that hydrophilics (blue sidechains) do want to be touching water, so they should be exposed as much as possible. Key word: Buried.

3. Clear the clashes
Two atoms can't occupy the same space at the same time. If you've folded a protein so two sidechains are too close together, your score will go down a lot. This is represented by a red spiky ball (clash) where the two sidechains are intersecting. If there are clashes, you know something is wrong with your protein. So make sure everything is far enough apart. Key word: Apart.
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Download and install Foldit

--- Quote ---To get started playing Foldit, download and install the game using one of the links below. If you haven't already, create a Foldit account. Your Foldit account lets you log in to the web site and the game. ...

Foldit runs on Windows (all versions since XP), macOS (10.7 or later), and Linux (64-bit). ...

The first time you play Foldit, the game starts in the first Intro Puzzle, "One Small Clash".

The Intro Puzzles show what a protein looks like, and how you can use the tools in Foldit to fix common problems. Most of the intro puzzles can be completed quickly, and none of them should take more than a few minutes. ...

Once you've finished the intro puzzles, or if you're in a hurry, you can start playing the science puzzles.

Each science puzzle runs for a specified time, usually a week. When a science puzzle ends, players receive "global points" based on how well they did. ...
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List of science puzzles

--- Quote ---1818: Coronavirus Binder Design: Round 5
Expires: 04/03/20 23:00:00

Design a binder against coronavirus! We're challenging players to design an antiviral protein that could bind to the 2019 coronavirus spike protein and disrupt viral infection. The starting structure is a solution designed by spvincent in our previous Round 2 puzzle. This solution makes an excellent interface with the target, but we're concerned that the binder may not fold properly. Our predictions suggest that the two sheets in this solution will not fold up as designed. We're asking Foldit players to try and improve this design so that it folds up correctly and can bind to the target! Players also have freedom to redesign an entirely new solution from scratch.

1817: Coronavirus ORF6 Prediction
Expires: 04/02/20 23:00:00

Refold this coronavirus protein! This protein is encoded in the viral genome of SARS-CoV-2, in a region called ORF6, but the protein's structure is still unknown. Evidence suggests this protein inhibits the natural immune response, helping the virus survive and replicate. If we knew how this protein folds, we might be able to figure out exactly how it inhibits the immune system. The puzzle's starting structure shows SS predictions from PSIPRED, and hints which parts of the protein might fold into helices or sheets. Refold this protein to find high-scoring solutions, which will tell us how this protein is most likely to fold!
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Mr. Bill:
If you're not into computer games, but your computer has some free time available, you can contribute to the Folding@home project.

--- Quote ---Folding@home (FAH or F@h) is a distributed computing project for simulating protein dynamics, including the process of protein folding and the movements of proteins implicated in a variety of diseases. It brings together citizen scientists who volunteer to run simulations of protein dynamics on their personal computers. Insights from this data are helping scientists to better understand biology, and providing new opportunities for developing therapeutics.
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Coronavirus – What we’re doing and how you can help

--- Quote ---Proteins are molecular machines that perform many functions we associate with life. ... Much like any other machine, it’s how a protein’s components are arranged and move that determine the protein’s function. In this case, the components are atoms.

Viruses also have proteins that they use to suppress our immune systems and reproduce themselves.

To help tackle coronavirus, we want to understand how these viral proteins work and how we can design therapeutics to stop them. ...

Our specialty is in using computer simulations to understand proteins’ moving parts. Watching how the atoms in a protein move relative to one another is important because it captures valuable information that is inaccessible by any other means. ...

...we simulated a protein from Ebola virus that is typically considered ‘undruggable’ because the snapshots from experiments don’t have obvious druggable sites. But, our simulations uncovered an alternative structure that does have a druggable site. Importantly, we then performed experiments that confirmed our computational prediction, and are now searching for drugs that bind this newly discovered binding site. ...

We want to do the same thing with coronavirus.
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Download Folding@home

--- Quote ---Available for: Linux, Windows, Mac

The Folding@home software runs while you do other things.

While you keep going with your everyday activities, your computer will be working to help us find cures for diseases like cancer, ALS, Parkinson’s, Huntington’s, Influenza and many others.

Please be patient if you experience idle time as we face the COVID-19 pandemic together! We are working like mad to start simulations of COVID-19 proteins. The enthusiastic response to our effort has been tremendous and has sometimes emptied our queues. This is a great “problem” to have as there is no end to the valuable science we can do, its just a matter of giving us some time to get more running.
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