PSC COVID-19 Update: June 15, 2020

Anton 2 Simulates Coronavirus Binding to Human Cells

A team at the University of Arkansas is using the unparalleled ability of the Anton 2 supercomputer to simulate molecular systems for microseconds or longer to better understand how the Coronavirus that causes COVID-19 attaches to human cells. Anton was developed by D. E. Shaw Research (DESRES) to execute molecular dynamics simulations of biomolecules such as proteins, nucleic acids and lipids orders of magnitude faster than was previously possible. The Anton 2 at PSC is provided without cost by DESRES for non-commercial use by the U.S. research community. PSC supports that community’s use of this resource with operational funding from the National Institutes of Health.

In order to infect a human cell, a virus must first break into it. The “spike” glycoproteins of the SARS-CoV-2 (COVID-19) and SARS-CoV (2002-03 SARS epidemic) viruses begin this process by first attaching to the same human cell-surface protein, ACE2. The University of Arkansas group, led by Mahmoud Moradi, is using Anton 2 to study the activation and deactivation of these spike proteins. Understanding the spike-protein activation process, and particularly gaining a dynamic understanding of how the protein behaves rather than a static picture, is key to the development of vaccines and drugs against COVID-19. While these processes occur over a time period of only millionths of a second (microseconds), the requirements of simulating them exceed the reach of general-purpose supercomputers. Anton 2’s specialized software and hardware make it uniquely suited to such simulations.

The researchers obtained time on Anton 2 via the COVID-19 HPC Consortium, of which PSC is a leading member. The consortium also allocates COVID-19 research time on PSC’s large Bridges supercomputing platform as well as other consortium-members’ computers. You can find information on applying for COVID-19 research time on Anton 2 here.

Anton 2 Simulations Examine Experimental COVID-19 Test

Scientists at the University of California, Riverside, are using the Anton 2 supercomputer to study the interactions of the SARS-CoV-2 virus’s genetic material with the proteins behind the CRISPR gene-editing system. They hope to use this information to develop an experimental test for the virus, which causes COVID-19. Anton was developed by D. E. Shaw Research (DESRES) to execute molecular dynamics simulations of biomolecules such as proteins, nucleic acids and lipids orders of magnitude faster than was previously possible. The Anton 2 at PSC is provided without cost by DESRES for non-commercial use by the U.S. research community. PSC supports that community’s use of this resource with operational funding from the National Institutes of Health.

Doctors need better and faster tests for identifying SARS-CoV-2 in suspected patients. A new version of the CRISPR gene-editing system called CRISPR-Cas holds promise as the backbone for such a test. A University of California, Riverside, group led by Giulia Palermo will use Anton 2 to study how the CRISPR-Cas protein recognizes viral genetic material. The task requires microsecond-long simulations, which are beyond the reach of most supercomputers. Anton 2’s specialized software and hardware, though, enables such simulations, allowing researchers to observe the changes in emerging CRISPR-Cas proteins that are required for detection of viral genes.

The researchers obtained time on Anton 2 via the COVID-19 HPC Consortium, of which PSC is a leading member. The consortium also allocates COVID-19 research time on PSC’s large Bridges supercomputing platform as well as other consortium-members’ computers. You can find information on applying for COVID-19 research time on Anton 2 here.

PSC Media Contacts

Media / Press Contact(s):

Kenneth Chiacchia
Pittsburgh Supercomputing Center
chiacchi@psc.edu
412-268-5869

Vivian Benton
Pittsburgh Supercomputing Center
benton@psc.edu
412.268.4960

Website Contact

Shandra Williams
Pittsburgh Supercomputing Center
shandraw@psc.edu
412.268.4960

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