Do you have a computer? Turn it on and join the research on the new coronavirus!

As long as you have a computer with internet access, you can also help fight the epidemic.

The following animation simulates the changing appearance of the spike glycoprotein of the new coronavirus in the real world. This protein is very important and is the key to the virus invading cells. This achievement will provide guidance for the development of antiviral drugs.

Dynamic simulation of the coronavirus spike glycoprotein. The coronavirus enters human cells by binding to the ACE2 receptor protein on human cells through the spike glycoprotein | Twitter: @Greg Bowman

You might think that this is generated by scientists using huge and expensive scientific instruments; but in fact, this result comes from the personal computers of hundreds of thousands of ordinary people. This project is called Folding@home (directly translated as "protein folding at home", the official website link can be found at the end of the article "Read the original text"), and you can also participate in it.

The story begins 20 years ago

In the 1960s, scientists began to use radio telescopes to listen to radio signals from space in search of traces of extraterrestrial intelligent life. Analyzing this data requires enormous computing power, and as the scale of the project expanded, the computing resources required for analysis became a bottleneck. So on the eve of the millennium, when the Internet was expanding to every corner of the world, they came up with an idea - to bring together computers from every household to complete computing tasks together.

SETI founder Frank Drake looks through data collected by radio telescopes | Lou Dematteis / Reuters

On May 17, 1999, SETI@home (Search for ExtraTerrestrial Intelligence at Home) was officially launched. This project was jointly run by programmers and astronomers from the University of California, Berkeley, and was one of the earliest "voluntary distributed computing projects." Participants in this project did not have to mail their computers to the university, but only needed to download the client. After the configuration was completed, when the computer entered the screen saver mode, it would automatically download the extraterrestrial wireless signal records from the server and search for greetings from extraterrestrial life.

Today, personal computers are more than 100 times faster than they were back then, so even if these computing tasks are performed at any time, it will not slow down the computer. Therefore, unlike the original SETI@Home, the current project is not limited to running only when the screen saver is on, but the choice of when to run is given to the user. Users can choose to run the project when other applications are not so active, or set it to run while doing other things.

"Volunteer distributed computing" can meet the needs of large-scale scientific computing. It combines the computing power of personal computers through the Internet. The huge computing tasks are divided into many small data packets on the server side and distributed to personal computers through the Internet; the personal computers complete the calculations separately and then send them back to the server for integration. You can think of "distributed computing" as a special supercomputer - traditional supercomputers are in a huge computer room, with a large number of processors connected by cables to complete computing tasks together; while voluntary distributed computing connects processors around the world through the Internet for computing.

The SETI@home project was suspended indefinitely on March 31 this year, but officials still encourage everyone to join other distributed computing projects, such as COVID-19 research | setiathome.berkeley.edu

In the twenty years since SETI@home began, this idea has been applied in various fields. Today, on the Berkeley Open Platform for Network Computing (BOINC), you can find projects from various disciplines, such as LHC@home for analyzing data from the Large Hadron Collider, Einstein@home for searching for gravitational waves from pulsars, and PrimeGrid for searching for large prime numbers. There are also many independent platforms, such as the Quake-Catcher Network for detecting earthquakes, and Folding@Home, which focuses on protein folding and dynamics, mentioned at the beginning of the article.

The scientists who developed SETI@home probably didn't expect that 20 years later, this technology would be used to fight a global plague. As you read this article, Folding@home is disassembling and distributing a large number of new coronavirus analysis tasks to computers around the world to help fight the epidemic.

Analyzing the dynamic image of proteins

A year and a half after SETI@home went online, when millions of volunteers' computers were listening to the sounds of the stars and searching for extraterrestrial life, Folding@home was released. Scientists hope to use the power of distributed computing to simulate protein folding, understand their role in disease, and provide information for the search for new drugs. In the past two decades, this project has helped to analyze abnormal kinases related to breast cancer, find potential drug targets for Ebola virus, and predict abnormal protein structures in Alzheimer's disease.

At the end of the 7100th day of the project's operation and the disastrous February of 2020, the team leader, biophysicist Greg Bowman, announced on the project's official website that they had begun to use Folding@home for work related to the new coronavirus protein, and subsequently increased the priority of computing tasks related to the new coronavirus protein.

Folding@home Team | foldingathome.org

The basic unit of protein is amino acid, but after amino acids are arranged into long chains, they need to fold into a three-dimensional structure to function. The folding process, the final structure, and the dynamics of the folded protein all affect the function of the protein and, in turn, life activities.

Scientists have many methods to analyze the static structure of proteins. For example, cryo-electron microscopy has shown the structure of the spike glycoprotein of the new coronavirus. However, these methods can only show the image of the protein at a specific moment. Bowman said: "The protein structure captured by the experimental method is like a photo of football players ready to go. It allows us to see the formation arrangement, but we can't see the whole game."

The static structure of a protein is like a photo of a football game: you can see the formation but not the actual game. | foldingathome.org

However, using these static images as a starting point and conducting computer simulations, it is possible to predict the movement of each atom in the protein, showing the areas that can change shape, allowing scientists to see the entire game and then formulate targeted offensive and defensive strategies. Take the Ebola virus as an example. In the past, people believed that the VP35 protein in it had no sites for drug action, but not long ago, computer simulations found that the new structures generated by dynamic changes are receptive to drug action [1], which suggests a new direction for finding treatments.

Similarly, when developing drugs to fight the new coronavirus, we may be able to find ideas in such research. The only problem is that such simulations require huge and expensive computing resources. The computers in biologists' offices may have to work non-stop for hundreds or even tens of thousands of years to simulate the dynamics of a protein.

Join us worldwide, you can

Fortunately, there are billions of personal computers around the world, and ordinary people who enthusiastically join the distributed computing network have made the time required to simulate protein dynamics acceptable.

In March, after the Folding@home project team issued a call on social media, many people joined the distributed computing network. The number of participating users has increased from about 30,000 in February to more than one million today. "Maybe everyone noticed the lag during installation," Bowman said on social networks, "There are so many people downloading the client that the server can't keep up. We are working hard to get the new server online."

Many PC hardware, video game-related manufacturers and media also called on users to join in | Twitter: @PC MASTER RACE

Although the computing power of each personal device is negligible, the huge number of them added together makes the available idle computing power exceed everyone's expectations. The most powerful supercomputer in the world is IBM's Summit, which can calculate 200 trillion times per second (2x10^17 times per second). On March 21, Bowman announced on social media that Folding@home's total computing speed was twice that of the Summit supercomputer. Just five days later, they were surprised to announce that the computing speed had exceeded 100 trillion times per second (10^18 times per second), an order of magnitude higher than the most advanced supercomputers. These computing powers are continuously invested in the research related to the new coronavirus protein. Simulation projects such as the spike protein-ACE2 protein complex, the new coronavirus protease, and the antibody protein are being continuously split and sent to participants around the world.

You can never have too much computing resources. In addition to washing your hands frequently, wearing a mask, and staying home as much as possible, anyone with a computer with Internet access can make further contributions to the fight against the epidemic. Go to the official website of the Folding@home project, download the client, install it, and start the program - at this point, your computer is ready to receive tasks and provide basic information for the development of special medicines.

The running interface of Folding@home. You can check on the official website that the task (PRCG: 13851) running at this time is a study related to SARS-CoV and SARS-CoV-2 | FAHControl

In addition, on the Berkeley University Open Platform for Network Computing (BOINC), the biomedical project Rosetta@home is also shifting its focus to coronavirus-related computing, and you can even run it on your smartphone.

The COVID-19 pandemic may be the worst plague since the 1918 influenza pandemic. This time, humans have a brand new weapon in their hands to fight the disease. It was once used to gaze at the endless starry sky, and now it will help us save lives looking up at the same starry sky.

More importantly, even ordinary people who know nothing about medicine and biology can contribute a little to wielding this blade. After all, there are billions of us, and I believe this power is enough to overcome all obstacles.

References:

[1] Cruz MA, Frederick TE, Singh S, Vithani N, Zimmerman MI, Porter JR, Moeder KE, Amarasinghe GK, Bowman GR. 2020. Discovery of a cryptic allosteric site in Ebola's 'undruggable' VP35 protein using simulations and experiments. bioRxiv:2020.02.09.940510.

[2] https://setiathome.berkeley.edu/

[3]https://www.theatlantic.com/science/archive/2017/05/aliens-on-your-packard-bell/527445/

[4] https://foldingathome.org/2020/02/27/foldinghome-takes-up-the-fight-against-covid-19-2019-ncov/

[5] https://foldingathome.org/2020/03/15/coronavirus-what-were-doing-and-how-you-can-help-in-simple-terms/

[6] https://www.dezeen.com/2020/03/25/coronavirus-cure-folding-at-home-software/

[7] https://medicine.wustl.edu/news/crowdsourced-supercomputing-project-sets-sights-on-coronavirus/

[8] http://boinc.bakerlab.org/rosetta/rah/rah_about.php

Author: Walnut seedlings

Editor: Mai Mai

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