One of the difficulties with dealing with a pandemic is that successfully battling the contagion can require taking actions that are diametrically opposed to what our own instincts want to do: Namely, to do something — either to protect ourselves or to protect those we care about. All of this is in direct contradiction to best medical practices, which calls for people to adopt social distancing techniques to the maximum extent possible.
There is, however, something you can do to help fight SARS-CoV-2, the coronavirus that causes the infection known as Covid-19: Contribute to Folding@Home. By downloading and installing the Folding@Home client, you can donate your spare CPU and GPU cycles to working on modeling. The Folding@Home team has made several blog posts from their efforts. The project was first explained in a Feb 23 post:
For both coronaviruses, the first step of infection occurs in the lungs, when a protein on the surface of the virus binds to a receptor protein on a lung cell. A therapeutic antibody is a type of protein that can block the viral protein from binding to its receptor, therefore preventing the virus from infecting the lung cell. A therapeutic antibody has already been developed for SARS-CoV, but to develop therapeutic antibodies or small molecules for 2019-nCoV, scientists need to better understand the structure of the viral spike protein and how it binds to the human ACE2 receptor required for viral entry into human cells.
The “other” coronavirus mentioned is SARS and 2019-nCoV was the old term for the virus now referred to as SARS-CoV-2. They continue:
Proteins are not stagnant—they wiggle and fold and unfold to take on numerous shapes. We need to study not only one shape of the viral spike protein, but all the ways the protein wiggles and folds into alternative shapes in order to best understand how it interacts with the ACE2 receptor, so that an antibody can be designed. Low-resolution structures of the SARS-CoV spike protein exist and we know the mutations that differ between SARS-CoV and 2019-nCoV. Given this information, we are uniquely positioned to help model the structure of the 2019-nCoV spike protein and identify sites that can be targeted by a therapeutic antibody. We can build computational models that accomplish this goal, but it takes a lot of computing power.
And the truth is? The combined computing power of human nerddom is capable of delivering performance that would blow Summit out of the water, though how much of it Folding@Home could practically leverage would be something of a question. It’s true that the speed of any single commodity system is going to be slow in comparison to the challenge. The speed of all of our commodity hardware, on the other hand, might actually make a difference.
In an updated blog post from March 10, John Chodera writes:
Folding@home team has released an initial wave of projects simulating potentially druggable protein targets from SARS-CoV-2 (the virus that causes COVID-19) and the related SARS-CoV virus (for which more structural data is available) into full production on Folding@home… This initial wave of projects focuses on better understanding how these coronaviruses interact with the human ACE2 receptor required for viral entry into human host cells, and how researchers might be able to interfere with them through the design of new therapeutic antibodies or small molecules that might disrupt their interaction.
The goal of the Folding@Home project is to target the most promising drug targets to find alternate conformations or “hidden pockets” — the sort that you can only find in simulation. Basically, Folding@Home wants to take the most likely candidates and then examine them with a fine-toothed comb to make sure no stone goes unturned. Download and install FAH, and you’ll be asked if you want to mine anonymously or for a team. If you don’t care about the entire “team” thing, you can just hit “Anonymous.” The application devotes to a web interface, but you can activate a desktop Advanced Control panel just by searching for “Folding.”
The basic control panel. I’ve only just started my own system mining again, after 15 years or so away.
“Any” is the default setting here, and it’s the right one. There isn’t a specific allocation for “Coronavirus” yet. From the tone of the blog posts, it sounds as if work on SARS-CoV-2 is still ramping up. No, contributing to a distributed computing project isn’t going to magically make a solution appear out of thin air — but we might make a difference to how long it takes to find a cure the scientific way. I’ll be bringing some testbeds online towards this purpose. Hope you’ll join me.
Oh. And please wash your hands.
Top image by NIAID-RML/CC BY SA 2.0
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