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Professor Receives National HPC Award for Simulations of COVID-19 “Spike” Protein

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STONY BROOK, NY, November 30, 2020 – Stony Brook University ‘s Carlos Simmerling, PhD, the Marsha Laufer Endowed Professor of Physical and Quantitative Biology, Professor of Chemistry, and Associate Director of the Laufer Center, and a team of scientists, received a national award for COVID-19 research in the field of high-performance computing. The award was announced at the SuperComputing 2020 (virtual) Conference. The award nominees included four scientific teams nationwide as the finalists. Simmerling’s team took the top spot.

Titled the Gordon Bell Special Prize for High Performance Computing-Based Covid-19 Research, the award recognizes “outstanding research achievement towards the understanding of the COVID-19 pandemic though the use of high-performance computing.” Teams nominated are “based on the performance and innovation in their computational methods, in addition to their contributions towards understanding the nature, spread and/or treatment of the disease.” This is the first year the Gordon Bell prize was also dedicated to COVID-19 related research.

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This schematic model developed by Simmerling and colleagues shows SARS-CoV-2, with the yellow/green being the spike and the yellow as the glycan shield. The smaller purple and mauve correspond to other viral surface proteins. The bottom layer is a simplified host cell surface with purple corresponding to ACE2 receptors to which the spike binds to activate infection.

The winning team centered their investigation on the virus’ “spike” protein, the known crown-like spike that enables the virus to infect human cells. They used the Summit supercomputer to simulate the SARS-CoV-2’s (SARS) spike protein and other viral properties that interact with the spike. The spike is the part of the virus targeted by the human immune system, and understanding the detailed behavior of the spike may provide important insight into how the spike may change as the virus mutates.

The team built atomic-detail models of the spike protein, along with models for the full virus with hundreds of millions of atoms. Then they used computer simulations on some of the world’s most powerful supercomputers to model how the flexible spike moves over time, providing a much more detailed view than is available from experiments. The simulations illuminate the job of the spike’s sugary gycan shield, which protects the virus against the host’s immune system and plays a critical role in the virus’ receptor binding domain.

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Carlos Simmerling, PhD

Professor Simmerling joined the national research collaborative, as his Stony Brook team had been working on computer simulation models to better understand how the spike protein changes shape as it goes about its job of unlocking the cell. The Simmerling research team includes graduate and undergraduate students working in his lab on the research. A broader description of this work and their computer modeling is detailed here.

“The power of using supercomputing to unravel aspects of SARS-CoV-2 that cannot be seen in such detail in lab experiments shows incredible promise for engineering-driven medical research and for discovering ways that we can treat not only COVID-19, but be better prepared to fight other coronaviruses and prevent future pandemics,” says Simmering. “I am honored to be part of this national collaborative HPC team recognized with this award.”

The award is accompanied by a $10,000 prize. The Special Prize for High Performance Computing-Based Covid-19 Research will be awarded in 2021 as well.

Research completed in the Simmerling lab that led to the award was supported in part by multiple funders, including the Department of Energy (DOE) through DOE’s Brookhaven National Laboratory, SUNY seed grant monies, and the Stony Brook University Office of the Vice President for Research.

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