With the worldwide coronavirus pandemic, scientists are creating a computer model of the virus to determine the mechanism the virus uses to infect the body. The first part of the model was done on the Frontera supercomputer at the University of Texas at Austin’s Texas Advanced Computing Center (TACC). According to the Top500 November 2019 rankings, Frontera is ranked as the fifth-best supercomputer in the world and the best academic supercomputer. The complete full model of the virus will help scientists design drugs and vaccines to combat the coronavirus.
Professor of chemistry and biochemistry at the University of California San Diego, Rummies Amaro, is at the forefront of designing an all-atom computer model of the coronavirus envelope. Viral envelopes are usually derived from proteins and comprise the outer layer of a virus, often helping the virus to avoid the host’s immune system. According to Amaro, “If we have a good model for what the outside of the particle looks like and how it behaves, we're going to get a good view of the different components that are involved in molecular recognition.” Molecular recognition is how the virus interacts with the angiotensin converting enzyme 2 (ACE2) receptors in the host.
Amaro used Frontera to run molecular dynamics simulations on about 250,000 processing cores, which is a massive undertaking. Says Amaro, “Simulations of that size are only possible to run on a machine like Frontera or on a machine possibly at the Department of Energy.”
Amaro continued, “These simulations will give us new insights into the different parts of the coronavirus that are required for infectivity. And why we care about that is because if we can understand these different features, scientists have a better chance to design new drugs; to understand how current drugs work and potential drug combinations work. The information that we get from these simulations is multifaceted and multidimensional and will be of use for scientists on the front lines immediately and also in the longer term. Hopefully, the public will understand that there are many different components and facets of science to push forward to understand this virus. These simulations on Frontera are just one of those components, but hopefully an important and a gainful one.”
Amaro’s study is published in the journal, ACS Central Science.