Supercomputers Enable Radical, Promising New COVID-19 Drug Development Approach

By Oliver Peckham

July 1, 2020

Around the world, innumerable supercomputers are sifting through billions of molecules in a desperate search for a viable therapeutic to treat COVID-19. Those molecules are pulled from enormous databases of known compounds, ranging from preexisting drugs to plants and other natural substances. But now, researchers at the University of Washington are using supercomputing power to revisit a decades-old concept that would allow researchers to design a completely new drug from the ground up.

This approach – called de novo protein design – works by linking amino acids together to create specific proteins. Thus far, de novo design has only been used for a few drugs that are still undergoing trial. In large part, de novo design has been stymied by the extreme difficulty in predicting how the amino acids in a protein would fold, making prediction of the full three-dimensional shape of the protein and other drug-critical factors exceedingly troublesome.

At the University of Washington’s Institute for Protein Design, David Baker – a professor of biochemistry and head of the institute – applied supercomputing to tackle this roadblock. Baker and his colleagues developed methods for the prediction of proteins’ folded forms and for the rapid design of targeted protein binders. The researchers use computer simulations to generate a library of candidates, after which the most promising candidates are tested in-depth in further simulations and wet labs.

For the last six months, the Baker Lab has been using this approach to zero in on COVID-19, predicting the folded shapes of millions of proteins and then matching them with various parts of the SARS-CoV-2 virus. This massive undertaking requires correspondingly massive computing – and for that, the researchers turned to Stampede2 at the Texas Advanced Computing Center (TACC). Stampede2 is a Dell EMC system with Intel Xeon Phi CPUs rated at 10.7 Linpack petaflops, which placed it 21st on the most recent Top500 list of the world’s most powerful supercomputers.

For their COVID-19 efforts, the team started by testing 20,000 “scaffold” proteins – starting points for drug design – each of which possesses more than a thousand possible orientations, with each orientation tested around a thousand times: in total, 20 billion interactions to test. The best million candidates from these went on to the second stage, sequence design, where the “scaffold” is covered in amino acids, with 20 possibilities at each position. 

In the third stage, the best hundred thousand protein candidates are forwarded to Agilent, a DNA synthesis firm, which returns physical DNA samples of those proteins that the Baker Lab can test against the real-life virus. Then, the team looks at the results and mutates individual amino acids on the proteins to see if docking performance improves or worsens. Then the proteins undergo a barrage of other tests and modifications, eventually resulting in the 50 promising leads that have been found so far.

“TACC has a lot of computing power and that has been really helpful for us,” said Brian Coventry, a PhD student working on the research, in an interview with TACC’s Aaron Dubrow. “Everything we do is purely parallel. We’re able to rapidly test 20 million different designs and the calculations don’t need to talk to each other.”

“Our goal for the next pandemic will be to have computational methods in place that, coupled with high performance computing centers like TACC, will be able to generate high affinity inhibitors within weeks of determination of the pathogen genome sequence,” Baker said. “To get to this stage will require continued research and development, and centers like TACC will play a critical role in this effort as they do in scientific research generally.”

Header image: antiviral protein binders (blue) targeting the spike proteins of the coronavirus. Image courtesy of Ian Haydon, Institute for Protein Design.

To read the reporting on this research from TACC’s Aaron Dubrow, 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!

Intel’s Optane/DAOS Solution Tops Latest IO500

August 11, 2020

Intel’s persistent memory technology, Optane, and its DAOS (Distributed Asynchronous Object Storage) stack continue to impress and gain market traction. Yesterday, Intel reported an Optane and DAOS-based system finishe Read more…

By John Russell

Summit Now Offers Virtual Tours

August 10, 2020

Summit, the second most powerful publicly ranked supercomputer in the world, now has a virtual tour. The tour, implemented by 3D platform Matterport, allows users to virtually “walk” around the massive supercomputer Read more…

By Oliver Peckham

Supercomputer Simulations Examine Changes in Chesapeake Bay

August 8, 2020

The Chesapeake Bay, the largest estuary in the continental United States, weaves its way south from Maryland, collecting waters from West Virginia, Delaware, DC, Pennsylvania and New York along the way. Like many major e Read more…

By Oliver Peckham

Student Success from ‘Scratch’: CHPC’s Proof is in the Pudding

August 7, 2020

Happy Sithole, who directs the South African Centre for High Performance Computing (SA-CHPC), called the 13th annual CHPC National conference to order on December 1, 2019, at the Birchwood Conference Centre in Kempton Pa Read more…

By Elizabeth Leake

New GE Simulations on Summit to Advance Offshore Wind Power

August 6, 2020

The wind energy sector is a frequent user of high-power simulations, with researchers aiming to optimize wind flows and energy production from the massive turbines. Now, researchers at GE are preparing to undertake a lar Read more…

By Oliver Peckham

AWS Solution Channel

AWS announces the release of AWS ParallelCluster 2.8.0

AWS ParallelCluster is a fully supported and maintained open source cluster management tool that makes it easy for scientists, researchers, and IT administrators to deploy and manage High Performance Computing (HPC) clusters in the AWS cloud. Read more…

Intel® HPC + AI Pavilion

Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change. Read more…

Research: A Survey of Numerical Methods Utilizing Mixed Precision Arithmetic

August 5, 2020

Within the past years, hardware vendors have started designing low precision special function units in response to the demand of the machine learning community and their demand for high compute power in low precision for Read more…

By Hartwig Anzt and Jack Dongarra

Intel’s Optane/DAOS Solution Tops Latest IO500

August 11, 2020

Intel’s persistent memory technology, Optane, and its DAOS (Distributed Asynchronous Object Storage) stack continue to impress and gain market traction. Yeste Read more…

By John Russell

Summit Now Offers Virtual Tours

August 10, 2020

Summit, the second most powerful publicly ranked supercomputer in the world, now has a virtual tour. The tour, implemented by 3D platform Matterport, allows use Read more…

By Oliver Peckham

Research: A Survey of Numerical Methods Utilizing Mixed Precision Arithmetic

August 5, 2020

Within the past years, hardware vendors have started designing low precision special function units in response to the demand of the machine learning community Read more…

By Hartwig Anzt and Jack Dongarra

Implement Photonic Tensor Cores for Machine Learning?

August 5, 2020

Researchers from George Washington University have reported an approach for building photonic tensor cores that leverages phase change photonic memory to implem Read more…

By John Russell

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

Machines, Connections, Data, and Especially People: OAC Acting Director Amy Friedlander Charts Office’s Blueprint for Innovation

August 3, 2020

The path to innovation in cyberinfrastructure (CI) will require continued focus on building HPC systems and secure connections between them, in addition to the Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

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

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... 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

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

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

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do Read more…

By Oliver Peckham

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

Neocortex Will Be First-of-Its-Kind 800,000-Core AI Supercomputer

June 9, 2020

Pittsburgh Supercomputing Center (PSC - a joint research organization of Carnegie Mellon University and the University of Pittsburgh) has won a $5 million award 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

Leading Solution Providers

Contributors

Nvidia’s Ampere A100 GPU: Up to 2.5X the HPC, 20X the AI

May 14, 2020

Nvidia's first Ampere-based graphics card, the A100 GPU, packs a whopping 54 billion transistors on 826mm2 of silicon, making it the world's largest seven-nanom Read more…

By Tiffany Trader

Australian Researchers Break All-Time Internet Speed Record

May 26, 2020

If you’ve been stuck at home for the last few months, you’ve probably become more attuned to the quality (or lack thereof) of your internet connection. Even Read more…

By Oliver Peckham

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k Read more…

By John Russell

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist Read more…

By Oliver Peckham

Joliot-Curie Supercomputer Used to Build First Full, High-Fidelity Aircraft Engine Simulation

July 14, 2020

When industrial designers plan the design of a new element of a vehicle’s propulsion or exterior, they typically use fluid dynamics to optimize airflow and in Read more…

By Oliver Peckham

John Martinis Reportedly Leaves Google Quantum Effort

April 21, 2020

John Martinis, who led Google’s quantum computing effort since establishing its quantum hardware group in 2014, has left Google after being moved into an advi Read more…

By John Russell

$100B Plan Submitted for Massive Remake and Expansion of NSF

May 27, 2020

Legislation to reshape, expand - and rename - the National Science Foundation has been submitted in both the U.S. House and Senate. The proposal, which seems to Read more…

By John Russell

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

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