Folding@home

by | May 14, 2020 | Essays

Scientists need your help in fighting the virus. Time to be a hero.

Proteins are long chains of amino acids that perform a vast array of functions within organisms. They differ from one another primarily in the sequence of their amino acids. These sequences typically fold into specific three dimensional structures that determine what the proteins do.

Viruses, including everybody’s new favorite, have proteins that suppress the immune system, help reproduce themselves, and so forth. Determining exactly how these proteins work is important in creating therapeutic treatments.

Vexingly, the proteins do not stand still. So what we get are snapshots—still images—of what a viral protein is up to. Imagine looking at a picture of players lined up on a soccer field at the start of the game. That might tell you a little bit about what’s going on, but it in no way captures the complexity of the game that’s to follow.

Folding@home uses computer simulations to understand proteins’ moving parts. This is akin to getting to watch the whole soccer game. Doing this gives scientists a chance to find weaknesses in the virus—places where we might be able use drugs to disrupt the viral proteins. Cool, right?

Now the problem: These computer simulations take massive computing power. How much computing power? It would take a single MacBook Pro about 500 years to power through all the calculations necessary to run a computer simulation for a protein. It would be helpful, scientifically speaking, to have results sooner than that.

Folding@home is a distributed computing project to help run the calculations for protein simulations, including that weaselly, COVID-19-causing coronavirus. If you’re willing to let the Folding@home software run in the background on your computer, it will chow through a few of the calculations. If we all run Folding@home on these calculations, well, you end up with the fastest supercomputer in the world. (How fast? Over 1 exaflop as of March 25—the only computer in the world that can hit 1 exaflop and about 6x faster than the world’s fastest traditional supercomputer.)

At MacAtoZ, we’ve got all our office machines running Folding@home with their spare processing cycles. What good is that? They’re contributing to research fighting COVID-19, specifically Project 13840:

NSP14, also known as ExoN, helps the SARS-CoV-2 coronavirus replicate its genome accurately while evading the host’s immune system. The protein performs two functions once the virus is inside of the host cell. First, it functions as an exonuclease, digesting RNA back into individual nucleotides. NSP14 is thought to use this activity to remove incorrect nucleotides when the protein copying the coronavirus’s RNA genome makes an error, ensuring that the copy is accurate. NSP14 can also add chemical tags known as methyl groups to the viral RNA, mimicking the tags found on normal cellular RNA. It is believed that this helps to camouflage the viral RNA from the host cell’s detection mechanisms, weakening or delaying the immune response to infection. Modeling the protein helps us better understand the role that its structural dynamics play in performing these functions. It also allows us to search for sites where antiviral drugs could bind to alter the protein’s structure and thereby inhibit its functioning. For more information, the New York Times put out the following overview of the coronavirus proteome: https://www.nytimes.com/interactive/2020/04/03/science/coronavirus-genome-bad-news-wrapped-in-protein.html

Now, I don’t know what any of that means. But I don’t have to, and you don’t either. Scientists need our help to fight COVID-19, what they need is computing power, and my God I’ve got that in spades. If you’re reading this, you probably do too.

So if you’d like to contribute, here’s what you do:

  1. Go to https://foldingathome.org
  2. Watch the video if you wish, then click the Start Folding button
  3. Download the appropriate Folding@home software (it should auto detect which type of computer you’re using)
  4. Install the software
  5. You can either run the software anonymously or set up a name. If you set up a name, you’ll be able to more easily track your contributions.
  6. If you want, you can join a team. My company is on Team: SMUG (255355), which is the local Salem Macintosh Users Group. Neither a name nor a team is required to participate.

Once you have the software installed, it will automatically take you to the web control panel at client.foldingathome.org. You can use this control panel to see details of your efforts, specify which disease you’re fighting (in addition to COVID-19 there’s Alzheimer’s, Cancer, Huntington’s, and Parkinson’s), adjust how much computing power you’re donating, and stop Folding if you need to.

I hope you’ll join me in the fight.