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Article | Argonne National Laboratory

Argonne’s COVID-19 research makes progress

COVID-19 research at Argonne continues at the laboratory’s Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science User Facility, to precisely determine the structures of the 28 unique proteins that make up the SARS-CoV-2 virus, which causes COVID-19. As these structures are determined, they are posted into an international Protein Data Bank (PDB), compiled by researchers around the world.

As of April 27, scientists using the APS have deposited 19 structures of SARS-CoV-2 viral proteins into the PDB. Additionally, two teams of researchers — one from the Scripps Research Institute in California and one from the University of Minnesota — have published papers on data they collected at the APS in February, and a third group from the Center for Structural Genomics of Infectious Diseases (led by Northwestern University, the University of Chicago and Argonne) has seen its research accepted for publication in Protein Science.

The Scripps group used a neutralizing antibody taken from a patient who contracted the previous SARS virus (SARS-CoV) from the 2002 outbreak and mapped it to the current SARS-CoV-2 virus, finding new insights into the way the novel virus recognizes antibodies. The group from the University of Minnesota studied the virus’s receptor recognition mechanism, which determines how contagious it is, in relation to the SARS virus of the early 2000s, providing guidance for today’s researchers seeking treatments. The Center for Structural Genomics group defined two additional crystal structures from the SARS-CoV-2 virus and compared them with those gathered from the SARS and MERS coronaviruses.

The APS is currently providing expedited, remote-access research, but only for experiments related to COVID-19 and critical pharmaceutical research at this time. As of April 27, there were 27 research groups from around the country using the APS’s ultra-bright X-rays to learn more about the virus and laying the groundwork for potential treatments for COVID-19.

Argonne’s supercomputing facilities are also contributing to the fight against COVID-19. Since the idea of establishing the COVID-19 High Performance Computing (HPC) Consortium was first federally proposed in late March, the consortium has received dozens of proposals and, as of May 1, had 36 projects up and running.

Among them is a nationwide collaboration that is applying artificial intelligence-driven biology to discover a treatment against COVID-19, led by Argonne computational biologist Arvind Ramanathan. His team aims to address the fundamental biological mechanisms of the virus and the disease and to identify potential therapeutics with the help of machine learning and deep learning techniques.

To date, the team has made significant progress toward its goals, including the development of artificial intelligence and machine learning tools that analyze millions of molecules to identify those that can bind to the virus’s known proteins.

The molecules that we identify at the end of our AI analysis are piped to our experimental collaborators,” Ramanathan said. We have sent out about 30 compounds that we are sharing with our collaborators at the University of Chicago and Frederick National Lab, among others, where testing is ongoing to see if these compounds do bind to these proteins that we are targeting.”

According to the project’s description on the consortium Web site, their approach uses HPC-tested open-source software and tools that will be released into the public domain — along with project data — to enable easy access, sharing and dissemination for further research. So far, nearly 80 terabytes of data have already been computed and made available, Ramanathan noted.

A well-coordinated effort between federal labs, universities and private research centers, the project’s backbone is a cadre of the world’s most powerful supercomputers, including Theta at the Argonne Leadership Computing Facility (ALCF), Summit at Oak Ridge Leadership Computing Facility (OLCF), Cori at Lawrence Berkeley National Laboratory’s National Energy Research Scientific Computing Center (NERSC), the Frontera and Longhorn supercomputers at the Texas Advanced Computing Center, and Comet at the San Diego Supercomputing Center.  ALCF, OLCF, and NERSC are DOE Office of Science User Facilities.

The Argonne Leadership Computing Facility provides supercomputing capabilities to the scientific and engineering community to advance fundamental discovery and understanding in a broad range of disciplines. Supported by the U.S. Department of Energy’s (DOE’s) Office of Science, Advanced Scientific Computing Research (ASCR) program, the ALCF is one of two DOE Leadership Computing Facilities in the nation dedicated to open science.

About the Advanced Photon Source

The U. S. Department of Energy Office of Science’s Advanced Photon Source (APS) at Argonne National Laboratory is one of the world’s most productive X-ray light source facilities. The APS provides high-brightness X-ray beams to a diverse community of researchers in materials science, chemistry, condensed matter physics, the life and environmental sciences, and applied research. These X-rays are ideally suited for explorations of materials and biological structures; elemental distribution; chemical, magnetic, electronic states; and a wide range of technologically important engineering systems from batteries to fuel injector sprays, all of which are the foundations of our nation’s economic, technological, and physical well-being. Each year, more than 5,000 researchers use the APS to produce over 2,000 publications detailing impactful discoveries, and solve more vital biological protein structures than users of any other X-ray light source research facility. APS scientists and engineers innovate technology that is at the heart of advancing accelerator and light-source operations. This includes the insertion devices that produce extreme-brightness X-rays prized by researchers, lenses that focus the X-rays down to a few nanometers, instrumentation that maximizes the way the X-rays interact with samples being studied, and software that gathers and manages the massive quantity of data resulting from discovery research at the APS.

This research used resources of the Advanced Photon Source, a U.S. DOE Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357.

Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science.

The U.S. Department of Energy’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit https://​ener​gy​.gov/​s​c​ience.