Supercomputer Research Probes Reengineering Old Antibodies to Fight SARS-CoV-2

By Oliver Peckham

July 30, 2020

As the COVID-19 pandemic progresses, the hunt for antibodies (the protective proteins produced by the human body in response to an infection) has reached a fever pitch. Researchers continue to struggle to reliably detect SARS-CoV-2 antibodies in patients who have recovered from COVID-19; they remain uncertain how long those antibodies last; and, most importantly, they are working around the clock to artificially produce those antibodies in patients who have not yet been infected by COVID-19. Now, a researcher from the Catholic University of America is looking at reengineering existing antibodies to fight the novel coronavirus.

“Antibodies are important because they prevent infection and heal patients affected by diseases,” said Victor Padilla-Sanchez, a researcher at The Catholic University of America, in an interview with Faith Singer-Villalobos at the Texas Advanced Computing Center (TACC). “If we have antibodies, we are immune to disease, as long as they are in your system, you’re protected. If you don’t have antibodies, then infection proceeds and the pandemic continues.”

Padilla-Sanchez is looking to the past – specifically, SARS-CoV – to inform the future. Both SARS-CoV and its current successor share the notorious spike protein that enables the viruses to infect human cells – so Padilla-Sanchez decided to examine whether the specific antibodies that could fight off SARS-CoV (named 80R and m396) could be modified to do the same for the current pandemic.

Padilla-Sanchez conducted detailed simulations of 80R and m396 using the Rosetta molecular docking software suite on two supercomputers: Bridges at the Pittsburgh Supercomputer Center (PSC) and Stampede2 (10.7 Linpack petaflops) at TACC. Finally, he generated high-resolution visualizations of the results on TACC’s Frontera supercomputer (23.5 Linpack petaflops), which currently ranks as the 8th most powerful publicly ranked supercomputer on the Top500 list. 

“XSEDE resources were essential to this research,” Padilla-Sanchez said. “Frontera has great performance when importing a lot of big data. We’re usually able to look at just protein interactions, but with Frontera and Bridges, we were able to study full infection processes in the computer.”

Docking between the modified 80R antibody and the SARS-CoV-2 spike protein. Image courtesy of Victor Padilla-Sanchez.

The simulations showed that certain key sequences prevent 80R and m396 from binding to the virus – but that amino acid substitutions might be able to improve binding interactions.

“We’re at the initial steps of this now, and this is where I’m hoping my work might help,” Padilla-Sanchez said. “Understanding why 80R and m396 did not bind to the SARS-CoV-2 spike protein could pave the way to engineering new antibodies that are effective. Mutated versions of the 80r and m396 antibodies can be produced and administered as a therapeutic to fight the disease and prevent infection.”

“Now,” he said, “I need to prove it in the lab.”

To read the article from TACC’s Faith Singer-Villalobos discussing this research, click here.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

UT Dallas Grows HPC Storage Footprint for Animation and Game Development

October 28, 2020

Computer-generated animation and video game development are extraordinarily computationally intensive fields, with studios often requiring large server farms with hundreds of terabytes – or even petabytes – of storag Read more…

By Staff report

Frame by Frame, Supercomputing Reveals the Forms of the Coronavirus

October 27, 2020

From the start of the pandemic, supercomputing research has been targeting one particular protein of the coronavirus: the notorious “S” or “spike” protein, which allows the virus to pry its way into human cells a Read more…

By Oliver Peckham

AMD Reports Record Revenue and $35B Deal to Buy Xilinx

October 27, 2020

AMD this morning reported record quarterly revenue of $2.8 billion and a finalized deal to buy FPGA-maker Xilinx for $35 billion in an all-stock transaction. The acquisition helps AMD keep pace during a time of consolida Read more…

By John Russell

Nvidia-Arm Deal a Boon for RISC-V?

October 26, 2020

The $40 billion blockbuster acquisition deal that will bring chip maker Arm into the Nvidia corporate family could provide a boost for the competing RISC-V architecture. As regulators in the U.S., China and the Europe Read more…

By George Leopold

OpenHPC Progress Report – v2.0, More Recipes, Cloud and Arm Support, Says Schulz

October 26, 2020

Launched in late 2015 and transitioned to a Linux Foundation Project in 2016, OpenHPC has marched quietly but steadily forward. Its goal “to provide a reference collection of open-source HPC software components and bes Read more…

By John Russell

AWS Solution Channel

Rapid Chip Design in the Cloud

Time-to-market and engineering efficiency are the most critical and expensive metrics for a chip design company. With this in mind, the team at Annapurna Labs selected Altair AcceleratorRead more…

Intel® HPC + AI Pavilion

Berlin Institute of Health: Putting HPC to Work for the World

Researchers from the Center for Digital Health at the Berlin Institute of Health (BIH) are using science to understand the pathophysiology of COVID-19, which can help to inform the development of targeted treatments. Read more…

NASA Uses Supercomputing to Measure Carbon in the World’s Trees

October 22, 2020

Trees constitute one of the world’s most important carbon sinks, pulling enormous amounts of carbon dioxide from the atmosphere and storing the carbon in their trunks and the surrounding soil. Measuring this carbon sto Read more…

By Oliver Peckham

AMD Reports Record Revenue and $35B Deal to Buy Xilinx

October 27, 2020

AMD this morning reported record quarterly revenue of $2.8 billion and a finalized deal to buy FPGA-maker Xilinx for $35 billion in an all-stock transaction. Th Read more…

By John Russell

OpenHPC Progress Report – v2.0, More Recipes, Cloud and Arm Support, Says Schulz

October 26, 2020

Launched in late 2015 and transitioned to a Linux Foundation Project in 2016, OpenHPC has marched quietly but steadily forward. Its goal “to provide a referen Read more…

By John Russell

Nvidia Dominates (Again) Latest MLPerf Inference Results

October 22, 2020

The two-year-old AI benchmarking group MLPerf.org released its second set of inferencing results yesterday and again, as in the most recent MLPerf training resu Read more…

By John Russell

HPE, AMD and EuroHPC Partner for Pre-Exascale LUMI Supercomputer

October 21, 2020

Not even a week after Nvidia announced that it would be providing hardware for the first four of the eight planned EuroHPC systems, HPE and AMD are announcing a Read more…

By Oliver Peckham

HPE to Build Australia’s Most Powerful Supercomputer for Pawsey

October 20, 2020

The Pawsey Supercomputing Centre in Perth, Western Australia, has had a busy year. Pawsey typically spends much of its time looking to the stars, working with a Read more…

By Oliver Peckham

DDN-Tintri Showcases Technology Integration with Two New Products

October 20, 2020

DDN, a long-time leader in HPC storage, announced two new products today and provided more detail around its strategy for integrating DDN HPC technologies with Read more…

By John Russell

Is the Nvidia A100 GPU Performance Worth a Hardware Upgrade?

October 16, 2020

Over the last decade, accelerators have seen an increasing rate of adoption in high-performance computing (HPC) platforms, and in the June 2020 Top500 list, eig Read more…

By Hartwig Anzt, Ahmad Abdelfattah and Jack Dongarra

Nvidia and EuroHPC Team for Four Supercomputers, Including Massive ‘Leonardo’ System

October 15, 2020

The EuroHPC Joint Undertaking (JU) serves as Europe’s concerted supercomputing play, currently comprising 32 member states and billions of euros in funding. I Read more…

By Oliver Peckham

Supercomputer-Powered Research Uncovers Signs of ‘Bradykinin Storm’ That May Explain COVID-19 Symptoms

July 28, 2020

Doctors and medical researchers have struggled to pinpoint – let alone explain – the deluge of symptoms induced by COVID-19 infections in patients, and what Read more…

By Oliver Peckham

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for hi Read more…

By Tiffany Trader

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

Aurora’s Troubles Move Frontier into Pole Exascale Position

October 1, 2020

Intel’s 7nm node delay has raised questions about the status of the Aurora supercomputer that was scheduled to be stood up at Argonne National Laboratory next year. Aurora was in the running to be the United States’ first exascale supercomputer although it was on a contemporaneous timeline with... Read more…

By Tiffany Trader

Is the Nvidia A100 GPU Performance Worth a Hardware Upgrade?

October 16, 2020

Over the last decade, accelerators have seen an increasing rate of adoption in high-performance computing (HPC) platforms, and in the June 2020 Top500 list, eig Read more…

By Hartwig Anzt, Ahmad Abdelfattah and Jack Dongarra

Leading Solution Providers

Contributors

European Commission Declares €8 Billion Investment in Supercomputing

September 18, 2020

Just under two years ago, the European Commission formalized the EuroHPC Joint Undertaking (JU): a concerted HPC effort (comprising 32 participating states at c Read more…

By Oliver Peckham

Nvidia and EuroHPC Team for Four Supercomputers, Including Massive ‘Leonardo’ System

October 15, 2020

The EuroHPC Joint Undertaking (JU) serves as Europe’s concerted supercomputing play, currently comprising 32 member states and billions of euros in funding. I Read more…

By Oliver Peckham

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia’s Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 “Accelerator Optimized” VM A2 instance family on Google Compute Engine. The instances are powered by the HGX A100 16-GPU platform, which combines two HGX A100 8-GPU baseboards using... Read more…

By Tiffany Trader

Microsoft Azure Adds A100 GPU Instances for ‘Supercomputer-Class AI’ in the Cloud

August 19, 2020

Microsoft Azure continues to infuse its cloud platform with HPC- and AI-directed technologies. Today the cloud services purveyor announced a new virtual machine Read more…

By Tiffany Trader

Oracle Cloud Infrastructure Powers Fugaku’s Storage, Scores IO500 Win

August 28, 2020

In June, RIKEN shook the supercomputing world with its Arm-based, Fujitsu-built juggernaut: Fugaku. The system, which weighs in at 415.5 Linpack petaflops, topp Read more…

By Oliver Peckham

HPE, AMD and EuroHPC Partner for Pre-Exascale LUMI Supercomputer

October 21, 2020

Not even a week after Nvidia announced that it would be providing hardware for the first four of the eight planned EuroHPC systems, HPE and AMD are announcing a Read more…

By Oliver Peckham

DOD Orders Two AI-Focused Supercomputers from Liqid

August 24, 2020

The U.S. Department of Defense is making a big investment in data analytics and AI computing with the procurement of two HPC systems that will provide the High Read more…

By Tiffany Trader

Oracle Cloud Deepens HPC Embrace with Launch of A100 Instances, Plans for Arm, More 

September 22, 2020

Oracle Cloud Infrastructure (OCI) continued its steady ramp-up of HPC capabilities today with a flurry of announcements. Topping the list is general availabilit Read more…

By John Russell

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This