Summit Supercomputer Models Coronavirus 'Spike'

March 12, 2020

By Bio-IT World Staff 

March 11, 2020 | As scientists across the globe bring their expertise to bear on the coronavirus pandemic, researchers in Tennessee are bringing big compute.

Researchers are using Summit, the world’s fastest supercomputer housed at Oak Ridge National Laboratory (ORNL), to identify compounds that may effectively combat the virus. Summit is powered by 9,216 IBM Power9 CPUs and over 27,000 NVIDIA V100 Tensor Core GPUs.

Viruses infect cells by binding to them and using a “spike” to inject their genetic material into the host cell. When Chinese researchers sequenced the novel coronavirus, they discovered that it infects the body by one of the same mechanisms as Severe Acute Respiratory Syndrome, or SARS.

Jeremy C. Smith, Governor’s Chair at the University of Tennessee (UT) and director of the UT/ORNL Center for Molecular Biophysics, wondered if the two viruses may even “dock” to the cell in the same way.

Team member and UT/ORNL CMB postdoctoral researcher Micholas Smith built a model of the coronavirus’ spike protein, also called the S-protein, based on early studies of the structure. “We were able to design a thorough computational model based on information that has only recently been published in the literature on this virus,” Smith said in an ORNL blog post.

With the help of the NVIDIA V100 GPUs, and GROMACS, a GPU-accelerated simulation package for biomolecular systems, the research team simulated 8,000 compounds in a matter of days to model which could impact the infection process by binding to the virus’s spike.

They identified 77 small-molecule compounds, such as medications and natural compounds, that have shown the potential to impair COVID-19’s ability to dock with and infect host cells. Since a highly accurate S-protein model was released in Science, the team plans to rapidly run the computational study again with the new version of the S-protein. This may change the ranking of the chemicals likely to be of most use. 

The 77 compounds need to be validated experimentally before any determinations can be made about their usability. “Summit was needed to rapidly get the simulation results we needed. It took us a day or two whereas it would have taken months on a normal computer,” said Smith.

“Our results don’t mean that we have found a cure or treatment for COVID-19. We are very hopeful, though, that our computational findings will both inform future studies and provide a framework that experimentalists will use to further investigate these compounds. Only then will we know whether any of them exhibit the characteristics needed to mitigate this virus.”

Summit gave the researchers its massive data processing capability, enabled by its 4,608 IBM Power Systems AC922 server nodes, each equipped with two IBM POWER9 CPUs and six NVIDIA Tensorcore V100 GPUs, giving it a peak performance of 200 petaflops, designed to be more powerful than one million high-end laptops.