you-can-help-fight-the-coronavirus.-all-you-need-is-a-computer

Staying
home isn’t the only way to help fight the coronavirus pandemic.

Hundreds
of thousands of volunteers have added their home computers to a vast network
that forms a virtual supercomputer called Folding@home. The Folding@home project, which uses
crowdsourced computing power to run simulations of proteins for researchers
studying diseases, announced in February that it would begin analyzing proteins
found in the coronavirus behind the ongoing
pandemic
(SN: 3/4/20).
These proteins are tools that help the virus infect human cells. Using computer
simulations, researchers are mapping the coronavirus’s proteins, in hopes of revealing
vulnerabilities that can be attacked with new drugs.

The more
volunteers who donate their unused computing power to the effort, the faster
the virtual supercomputer can work its magic. Since the project announced its new focus on the coronavirus, around 400,000
new volunteers have joined.

Science
News
spoke with
project leader Gregory Bowman, a biophysicist at Washington University School
of Medicine in St. Louis, about how the project works and how people can help.


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How do simulations help map coronavirus proteins?

Researchers
have taken snapshots of the proteins of the coronavirus, called SARS-CoV-2,
using techniques like X-ray crystallography and cryo-electron microscopy (SN: 10/4/17). But proteins
don’t hold still, Bowman says.

“All the
atoms in the protein and [its surroundings] are continually pushing and pulling
on each other,” he says. “What we’re doing is modeling those physical
interactions in the computer.” Those simulations reveal the different shapes a protein’s
structure can take.

What kinds of vulnerabilities are you looking for?

“You
want a nice pocket on the surface of a protein where you can imagine this
little molecule that we design inserting into a groove,” Bowman says. But many
proteins, particularly those in viruses, have seemingly smooth surfaces, making
them hard to target.

Folding@home
simulations give scientists a chance to uncover what Bowman calls “cryptic
pockets” — potential docking sites for drugs that aren’t visible in still
images of the protein, but are revealed as the protein wriggles around in a computer
simulation.


The Folding@home project aims to simulate “every [coronavirus] protein we can build reasonable starting structures for,” Bowman says. “There’s already a number of proteins from the novel coronavirus” that researchers have imaged, such as the virus’s spike protein (shown), which helps it infect human cells. Folding@home is simulating coronavirus proteins like this one to search for drugs that could stop the virus.

Has this worked for other viruses?

“We
actually took one protein from the Ebola virus and ran simulations and discovered one of these cryptic
pockets
,” Bowman
says. “Then we went and did the experiments to show that there really is a
small pocket, and if we stick a small molecule in there, it really can shut the
protein’s function off.” Likewise, a new drug molecule could be designed to
stick in the chemical cogs of a SARS-CoV-2 protein that renders the virus unable
to infect human cells.

Why not just find an existing drug that works for the coronavirus?

“That
would be amazing,” Bowman says. Developing new drugs can take years or even
decades, so researchers are investigating several existing
drugs

— such as those
designed to fight hepatitis C, Ebola and malaria — as potential COVID-19
treatments (SN: 3/10/20). But “there’s no guarantees that these things
will work,” he says. For instance, antiviral drugs used to treat HIV that
initially looked promising showed no clear benefit for
coronavirus patients

in a recent clinical trial (SN: 3/19/20). Efforts like Folding@home
supplement tests on existing drugs by expanding the search.

Even if
someone does identify a drug that can cripple SARS-CoV-2, “we don’t want to
stop there,” Bowman says. “The assumption is that, like many viruses, this is
going to mutate pretty fast, and that if we don’t keep up with it, we’ll be
right back with the same problem we have now. Tackling this thing on many
fronts is our best bet for success.”

Why do you need a supercomputer for the simulations?

“We have
to work on very, very, very small timescales” to capture the tiny jitters of
atoms in proteins, Bowman says. “Each step in the simulation is on the order of
a femtosecond,” or one quadrillionth of a second. To track protein motion over,
say, a second, “we’ve got to do like a billion-squared operations on the
computer, and each of those operations requires us to ask how every pair of
atoms in the protein and surrounding solution are interacting with each other,”
he says. By drawing on the computing power of many volunteers at once,
Folding@home performs calculations in a single month that could take an
ordinary desktop computer 100 years.

Folding@home
isn’t the only supercomputer put to the task of studying SARS-CoV-2. On March
23, the White House announced a new consortium of companies, universities and
government agencies — including several national laboratories, NASA, IBM and
Microsoft — that are offering researchers access to their supercomputers to expedite
the discovery of treatments or a vaccine for SARS-CoV-2.

Who can help with Folding@home?

“Anyone can install our software on their personal computers and contribute” some of their unused computing power, Bowman says. “We’ve got everyone from people running it on their older laptops, to gamers that have really hardcore machines to … businesses who are pointing computer clusters at Folding@home.”


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