A computer’s all you need: [email protected] joins the race to find a COVID-19 cure

Exploring a Stanford-led research project’s progress towards fighting the pandemic

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“Today, you just need a computer … That’s all you need. You don’t need to have a fancy computer [or a] super modern computer. Anything will do,” said Anton Thynell, head of collaboration and communication at [email protected]

Founded by chemistry, structural biology and computer science professor Vijay Pande in 2000 at Stanford, the global computing research community [email protected] (FAH) is now joining the race to find a cure for COVID-19. Volunteers from across the globe are downloading the FAH software, which is accessible to everyone, to run simulations of protein-folding in the background of their computer. The simultaneous running of these simulations contributes to researchers’ efforts to find treatments to certain diseases, illnesses and COVID-19. 

[email protected] was originally a computing project that studied and simulated biomolecular systems. In 2006, collaborators from Stanford University joined the project and later increased computing performance to a level that rivaled that of a supercomputer. 

Upon downloading the FAH software, volunteers are given specific proteins to run simulations on. They then can start folding by running their extra CPU power — a part of the computer that operates instructions — and later, they upload the results. The word “folding” comes from the process that proteins undergo when they are created. During that process, protein molecules “transform from a long chain of amino acids to a complex shape (it ‘folds up’).” The resulting structure allows researchers to understand the proteins’ properties and functions. 

The FAH community aims to apply their professional knowledge along with volunteers’ computing power to “understand the role of proteins’ dynamics in their function and dysfunction, and to aid in the design of new proteins and therapeutics.” It is established as the world’s fastest supercomputer according to Ethan Zuo, president of [email protected] — a group of volunteers who contribute to the [email protected] research project.

Thynell, who joined the [email protected] community in 2013, said that since COVID-19 began, he and his team have created a separate project that relied on the [email protected] concept to understand SARS-CoV-2. 

“[COVID-19] was really an all-hands-on-deck situation,” Thynell said. “I stopped working at my regular job and started full-time at [email protected] We grew our community [to] about 150 times [our past size] in three months. That’s where we are today.” 

Thynell broke down the process and importance of understanding protein dynamics when trying to find treatments or solutions to diseases, pandemics and more. 

“Most of the time, when you’re studying biology, you look at proteins as a fixed structure, but they’re actually moving around,” Thynell said. “And there are tons of reactions happening in our cell structure all the time. So these proteins are actually like small machines … We wanted to understand more about the virus and hopefully find some hidden pockets. It’s like a treasure map, and sometimes you find a treasure.”

“These hidden pockets can open up for a certain period of time and you can look at them at potential[ly] druggable sites, which is very interesting for developing therapeutics,” he added. 

Zuo added that [email protected] is helping researchers study spike proteins, a type of protein that is part of the SARS-CoV-2 and allows the coronavirus to enter host cells. Zuo states that using extra computing power to run simulations of the virus can speed up the process of studying how these proteins work, which can then help researchers find ways to manipulate them using medicine.

“When you download our software from our website and you have Wi-Fi or internet, you connect with our servers and download the small work unit —that’s a small part of a large simulation — and your computer starts crunching away at it,” Thynell said. “You can decide how much computing power you want to dedicate or when you want to start. It’s all up to you.”

Recently, Zuo has been very active in volunteering for the [email protected] COVID-19 project. He leaves his computer on 24 hours a day so that it can build computational models to help identify sites of the spike protein that researchers can target through a therapeutic antibody.

“[When] school shut down, everyone was doing online learning,” Zuo said. “When doing online learning, I realized that everyone is using their computers for a large fraction of the day … [but] not 100% of their computing potential is used. So I decided to [help] put that extra compute power to good use … Even though [email protected] is the world’s largest supercomputer, a surprising number of people don’t know about [it].”

“By reaching out to more people, you’ll make the supercomputer more powerful [in] finding a cure for COVID-19 more quickly and gain knowledge more effectively,” he added. 

Recently, [email protected] has been working with COVID Moonshot—an organization aiming to develop inexpensive patent-free therapeutics for COVID-19 — to identify key compounds that may stop the main viral protease (Mpro), an enzyme that breaks down proteins of COVID-19. As of now, over 800 compounds have been simulated and tested. Volunteers are actively participating in weekly sprints in which they donate their computing power to crunching work units to collect and generate new designs for proteins. Additionally, researchers are constantly discovering new things about the virus and are actively publishing them on their home website

To see and measure progress within [email protected] teams, volunteers are able to collect individual points for their contributions, which are displayed on a universal leaderboard. Depending on the computation power and system, certain amounts of points may also be awarded to teams, which puts them higher on the leaderboard. 

According to Thynell, the leaderboard also shows what communities are participating in folding; these include tech companies such as Google, Reddit, Linus, NVIDIA and Intel. Global teams include China [email protected] Power, Overclockers Australia and TSC Russia.

“What was really interesting is that [email protected] is global,” Thynell said. “We have people contributing from every part of the world. And it’s really amazing to see a global community coming together and fighting the virus, with the spare computing power of your home computer. That has been really nice to see.”

Contact Rachel Jiang at  racheljiang310 ‘at’ gmail.com

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Rachel was a high school intern for The Daily in summer 2019.