Researchers investigating some of humanity’s most vexing diseases began reaching out 20 years ago to nerds, gamers and even giant high-tech corporations across the world, hoping to borrow unused time on their computers. They signed up thousands, who donated their computing power so the scientists could better research cancer, Alzheimer’s and the Ebola virus, among others.
Now those scientists have turned their attention to the new coronavirus.
Washington University researchers, who are leading the project, are running complex computer simulations that model the building blocks of the new coronavirus in 3-D. But with the cost of supercomputing time astronomically expensive and equally hard to reserve, and researchers needing even more power, the team has again turned to the computers of the world for help.
Millions have responded.
Large technology companies — including Microsoft, Avast, Amazon Web Services, Pure Storage, AMD, VMware, Cisco, Oracle and the European Organization for Nuclear Research, which runs the Large Hadron Collider, the world’s most powerful particle accelerator — have offered their vast computing resources.
Even La Liga, the Spanish professional soccer league, redirected its supercomputer’s resources from spotting illegal broadcasts of games to protein folding.
Since March, the project has grown more than 100 times to as many as 5 million users and has created the fastest “supercomputer” in the world by a factor of 10, said Washington U. molecular biophysics professor Greg Bowman, who is leading the team.
Altogether, the computers’ peak performance: 2.5 exaFLOPS, or more than 2.5 quintillion operations each second. Bowman’s project, called Folding@home, did what technology companies and the federal government had been racing to do for many years.
“It’s pretty ridiculous,” Bowman said. “One of my childhood dreams was to have the world’s fastest computer. I think I had video games in mind. But this works too.”
A menacing monster
Originally based out of Stanford University, Folding@home has operated for nearly 20 years, focusing on other diseases and contributing to over 300 published research papers. Philadelphia’s Temple University and New York City’s Memorial Sloan Kettering Cancer Center are part of the project, too.
But when it became clear that COVID-19 was going to become a pandemic in early March, the project pivoted to focus almost exclusively on the virus.
Folding@home helps Bowman’s lab run computer simulations to visualize the coronavirus’ proteins — molecular building blocks, too tiny to see with any microscope. By understanding the 3D structure of these proteins and how they move around, they can identify weaknesses that medicines can exploit.
The complex computations required to run these simulations would take the average computer more than 100 years, but by distributing the workload among users — who have downloaded the software onto their personal machines, and call themselves “folders” — the simulations take a fraction of the time.
Relying on a process known as “distributed computing,” the software works by fetching a small processing job from the organization’s servers, running its computations, and then returning results to researchers. Users call it “folding.” When done, the software fetches the next job.
Bowman’s team has focused on disarming the coronavirus’ main attack mechanism — spiky proteins that protrude from the virus’ surface to bind with receptors on their prey. The virus, called SARS-CoV-2, uses its spike protein to bind with a specific receptor called ACE2, which normally helps regulate blood pressure.
To clamp down on ACE2, the spiky protein must first open, almost like a mouth would. The virus is not a neat sphere as is often depicted, Bowman said, but instead has a surface that rises and falls “like some Medusa.”
“Quite a dynamic and menacing looking little monster,” he said.
Bowman’s lab plans to release a draft of a research article next week summarizing what it has learned the last few months. As a result of the sheer amount of data his lab has processed, the raw dataset referenced in the paper is 100,000 times bigger than typical, he said.
“The scale of the dataset is off the charts,” he said.
Part of the team
Amanda Blevins, chief technologist at Silicon Valley cloud computing company VMware, said she found out about the software in March.
“I can’t speak for all gamers, but I can’t game 24 hours a day,” she said. “I have a high-end machine sitting next to me, so I figured I’d take advantage of it.”
Blevins tweeted about the software, and within weeks, she had recruited more than 1,000 coworkers at VMware to join the effort. The software rewards points for every job it runs, incentivizing users to continue contributing to the project. Users can also rack up points in teams, with leaderboards updated daily.
“We like to be competitive in addition to supporting a good cause,” said Blevins, whose sister is a nurse at a COVID-19 unit at a hospital in Colorado. “We’re about to move into 25th place overall, and we weren’t even on the leaderboards in March.”
Graduate student Sukrit Singh, who works in Bowman’s lab, credits the project’s success to a dedicated user base, particularly a core group of around 30 users who have stuck with the project since its conception nearly 20 years ago.
“They feel like they’re a part of the research team,” Singh said. “Some have even attended our PhD defenses virtually.”
Users said that while folding helps contribute to scientific research, they take something personal away from it, too.
“The helplessness that we all feel right now is so out of our control,” said Emma Matthies of Minnesota. “But this is something that we can do that feels like it’s contributing to an actual scientific effort to improve the situation.”
Matthies, who works a full-time job in information security, volunteers upward of two hours a day on the project, in part to help run an online community of folders on the messaging platform Discord.
Folders frequently post screenshots of the proteins they help render onto Discord. Matthies, who does not come from a background in biology, said she has learned a lot because researchers like Singh help explain what users are looking at.
Singh said the community has helped reaffirm that the Internet can be a force for good.
“One my big fears is that the Internet has an element of divisiveness and toxicity,” he said. “But the community here has really rallied around this cause.”
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