Posts Tagged ‘Protein Data Bank’

Supercomputers Battle COVID-19

May 22, 2020

When the world finally defeats the coronavirus and Covad-19, a small part in the victory will go to massive computer power. As Dario Gil, Director of IBM Research, noted; 16 systems with more than 400 petaflops, 775,000 CPU cores, 34,000 GPUs, and counting are among the firepower.

Back in March DancingDinosaur reported here that IBM’s Summit, which the company was boasting as the world’s most powerful supercompter was able to simulate 8,000 chemical compounds in a matter of days in a hunt for something that could impact the COVID-19 infection. 

Writing this today, late in May, we already know that teams of medical researchers, scientists, technology experts, and a vast array of talents are working almost non-stop to find, develop, test, and mass produce a cure, with luck in the form of a vaccine. We should also note all the countless nurses, doctors, aides, assistants and various hospital and food and logistics staff of all types and outside support roles who are involved in keeping things working, feeding staff, wheeling patients around, and otherwise helping to save lives.

As Gil explains: high-performance computing systems allow researchers to run very large numbers of calculations in epidemiology, bioinformatics, and molecular modeling–all the required science disciplines that need to be involved in whatever success is ultimately achieved. You can probably throw in chemistry and a few other areas of electronics and engineering as well. Without massive computer horsepower these experiments would take years to complete if worked by hand, or months if handled on slower, traditional computing platforms.

These machines—more than 25 U.S.-based supercomputers with more than 400 petaflops of computing power—are now available for free to those working toward a vaccine or treatment against the virus, through the COVID-19 High Performance Computing Consortium.

It was created with government, academia and industry—including competitors, working side by side. IBM is co-leading the effort with the U.S. Department of Energy, which operates the National Laboratories of the United States. Google, Microsoft, Amazon, and Hewlett Packard Enterprise have joined, as well as NASA, the National Science Foundation, Pittsburgh Supercomputing Center, and six National Labs—Lawrence Livermore, Lawrence Berkeley, Argonne, Los Alamos, Oak Ridge, and Sandia, and others. And then there are academic institutions, including MIT, Rensselaer Polytechnic Institute, the University of Texas, Austin, and the University of California, San Diego.

The White House has been getting deservedly bashed for its slowness, incompetence, and narrow-minded bungling. However, Gil reports the White House’s Office of Science and Technology Policy has taken up an effort that can make a real difference. He adds; I want to offer this promise: IBM will continue to explore everything in our power to use our technology and expertise to drive meaningful progress in this global fight.

The first thing Gil’s team did was to spread the word to people who might be working on this on any or all fronts—from drug discovery and development with AI-led simulations to genomics, epidemiology and health systems.

He goes on:  We need to understand the whole life cycle of this virus, all the gearboxes that drive it—how it encounters and infects the host cell and replicates inside it, preventing it from producing vital particles. We need to know the molecular components, the proteins involved in the virus’ biochemistry, and then to use computational modeling to see how we can interrupt the cycle. That’s the standard scientific methodology of drug discovery, but we want to amplify it and speed it up.

The virus has been exploding in humans for months, providing an abundance of samples for computer modeling and analysis, Gil continued. Scientists already are depositing samples into public data sources such as GenBank and Protein Data Bank. There are many unknowns and assumptions but a lot of proposals involve using the available protein structures to come up with potential molecular compounds that could lead to a therapeutic treatment or a vaccine. Let’s hope they have great success, the sooner the better.

DancingDinosaur is Alan Radding, a veteran information technology analyst, writer, and ghost-writer. Follow DancingDinosaur on Twitter, @mainframeblog, and see more of his work at

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