Over the course of the last year, many detailed computational models of SARS-CoV-2 have been produced with the help of supercomputers, but those models have largely focused on critical elements of the virus, such as its notorious spike proteins. Now, researchers at the University of Chicago have used supercomputing power to generate the first computational model of the entire SARS-CoV-2 virus.
The team settled for a coarser model, but still aimed to include key characteristics of each facet of the virus. As a result, the resolution fell short of the atomic-level modeling conducted by many institutions last year, but the researchers managed to capture a much wider view of the virus.
“The virus itself is a holistic thing,” said Gregory Voth, a computational scientist and professor of chemistry at the University of Chicago who led the team that conducted the research, in an interview with Louise Lerner. “In my opinion, you can’t assume you can look at individual parts in isolation. Viruses are more than just the sum of their parts.”
“You could try running an atom-level model of the actual entire virus, but computationally it would bog you down immediately,” he explained. “You might be able to manage it long enough to model, say, a few hundred nanoseconds worth of movement, but that’s not really long enough to find out the most useful information.”
To create the model, the researchers made use of a medley of computing resources. In addition to in-house resources from the University of Chicago’s Research Computing Center, they also worked with the Frontera system at the Texas Advanced Computing Center (TACC) and the Anton 2 system at the Pittsburgh Supercomputing Center (PSC).
Voth says that the resulting model will help answer more complex, holistic questions about how SARS-CoV-2 operates. “One of the main things you might want to know is, do you need to dose every spike protein for it to work? If not, how low a percentage can you get away with?” he said.
The researchers have made the complete model available for download here, and they hope that it will prove useful for researchers around the world as they study the operation and evolution of the coronavirus.
“Making a multiscale model of the whole virus and integrating all this information rapidly is a big technological step forward,” he said. “I’m really proud of my lab. We did it in record time, really—just a few months. If there is any upside to this pandemic, I hope that it advances our tools to fight viruses beyond COVID-19—like influenza, HIV and any new coronaviruses that arise in the future.”
To read the reporting from the University of Chicago’s Louise Lerner, click here.