Supercomputer-Powered Protein Simulations Approach Lab Accuracy

By Oliver Peckham

June 1, 2020

Protein simulations have dominated the supercomputing conversation of late as supercomputers around the world race to simulate the viral proteins of COVID-19 as accurately as possible and simulate potential bindings in the hopes of finding a therapeutic to treat the pandemic. Even in many supercomputer-powered protein simulations, however, the computer work is still a stepping stone to lab work, which tends to be more accurate. Now, new work powered by Extreme Science and Engineering Discovery Environment (XSEDE) supercomputers is challenging that, with researchers at Michigan State University producing predictions that rival the most precise lab measurements.

The researchers – Michigan State University’s Lim Heo (a postdoctoral fellow) and Michael Feig (his advisor) used molecular dynamics simulations to refine existing predictions made by other research groups. Many of the protein simulations conducted, it turned out, still had the proteins in forms that exerted unnecessary energy – and thus, did not represent the proteins truly at rest. 

“Proteins carry out biological functions. You can measure and analyze those functions, but to really understand them you have to look at the details of how proteins operate,” Feig told XSEDE’s Ken Chiacchia in an interview. “We know a lot of structures from experiments, but haven’t [done this, for example, with] most of the proteins in bacteria. We need to fill the gap by generating models quickly and efficiently.”

The Michigan State duo took a set of 27 predicted protein structures (generated by researchers at the 13th Critical Assessment of Techniques for Protein Structure Prediction competition in 2018) and used molecular dynamics to simulate those predicted structures over a longer time period, essentially allowing them to settle into their most natural states. 

After refining the predicting structures, the researchers found that accuracy had been improved across the board, between three and 30 percent for every structure. On the higher end of this range, the predicted structures came close to the accuracy of x-ray based lab analysis of proteins.

An example of one of the resulting structures (red and blue) superimposed on the laboratory measurement (yellow and pink).

Of course, simulating those protein structures over a long period requires immense computing power. For that, the research team turned to the GPU nodes on a pair of supercomputers allocated through XSEDE: the Pittsburgh Supercomputing Center’s Bridges system, which delivers 1.35 peak petaflops, and the San Diego Supercomputer Center’s Comet system, which delivers 2.76 peak petaflops. 

“Our modeling efforts are compute-intensive,” Feig explained. “XSEDE resources provided a significant amount of the resources we need to achieve significant model improvements. In brief, we can improve protein structures more with more computing time. Having access to XSEDE resources in addition to our local resources allowed us to improve structures than what we could have done otherwise.”

Next, the researchers are aiming to optimize their simulations in order to run them for longer simulated periods to increase the accuracy even more.

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!

Supercomputer Research Reveals Star Cluster Born Outside Our Galaxy

July 11, 2020

The Milky Way is our galactic home, containing our solar system and continuing into a giant band of densely packed stars that stretches across clear night skies around the world – but, it turns out, not all of those st Read more…

By Oliver Peckham

Max Planck Society Begins Installation of Liquid-Cooled Supercomputer from Lenovo

July 9, 2020

Lenovo announced today that it is supplying a new high performance computer to the Max Planck Society, one of Germany's premier research organizations. Comprised of Intel Xeon processors and Nvidia A100 GPUs, and featuri Read more…

By Tiffany Trader

Xilinx Announces First Adaptive Computing Challenge

July 9, 2020

A new contest is challenging the computing world. Xilinx has announced the first Xilinx Adaptive Computing Challenge, a competition that will task developers and startups with finding creative workload acceleration solutions. Xilinx is running the Adaptive Computing Challenge in partnership with Hackster.io, a developing community... Read more…

By Staff report

Reviving Moore’s Law? LBNL Researchers See Promise in Heterostructure Oxides

July 9, 2020

The reality of Moore’s law’s decline is no longer doubted for good empirical reasons. That said, never say never. Recent work by Lawrence Berkeley National Laboratory researchers suggests heterostructure oxides may b Read more…

By John Russell

President’s Council Targets AI, Quantum, STEM; Recommends Spending Growth

July 9, 2020

Last week the President Council of Advisors on Science and Technology (PCAST) met (webinar) to review policy recommendations around three sub-committee reports: 1) Industries of the Future (IotF), chaired be Dario Gil (d Read more…

By John Russell

AWS Solution Channel

Best Practices for Running Computational Fluid Dynamics (CFD) Workloads on AWS

The scalable nature and variable demand of CFD workloads makes them well-suited for a cloud computing environment. Many of the AWS instance types, such as the compute family instance types, are designed to include support for this type of workload.  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…

Penguin Computing Brings Cascade Lake-AP to OCP Form Factor

July 7, 2020

Penguin Computing, a subsidiary of SMART Global Holdings, Inc., announced yesterday (July 6) a new Tundra server, Tundra AP, that is the first to implement the Intel Xeon Scalable 9200 series processors (codenamed Cascad Read more…

By Tiffany Trader

Max Planck Society Begins Installation of Liquid-Cooled Supercomputer from Lenovo

July 9, 2020

Lenovo announced today that it is supplying a new high performance computer to the Max Planck Society, one of Germany's premier research organizations. Comprise Read more…

By Tiffany Trader

President’s Council Targets AI, Quantum, STEM; Recommends Spending Growth

July 9, 2020

Last week the President Council of Advisors on Science and Technology (PCAST) met (webinar) to review policy recommendations around three sub-committee reports: 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

Q&A: HLRS’s Bastian Koller Tackles HPC and Industry in Germany and Europe

July 6, 2020

In this exclusive interview for HPCwire – sadly not face to face – Steve Conway, senior advisor for Hyperion Research, talks with Dr.-Ing Bastian Koller about the state of HPC and its collaboration with Industry in Europe. Koller is a familiar figure in HPC. He is the managing director at High Performance Computing Center Stuttgart (HLRS) and also serves... Read more…

By Steve Conway, Hyperion

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time Read more…

By John Russell

Hyperion Forecast – Headwinds in 2020 Won’t Stifle Cloud HPC Adoption or Arm’s Rise

June 30, 2020

The semiannual taking of HPC’s pulse by Hyperion Research – late fall at SC and early summer at ISC – is a much-watched indicator of things come. This yea Read more…

By John Russell

Racism and HPC: a Special Podcast

June 29, 2020

Promoting greater diversity in HPC is a much-discussed goal and ostensibly a long-sought goal in HPC. Yet it seems clear HPC is far from achieving this goal. Re Read more…

Top500 Trends: Movement on Top, but Record Low Turnover

June 25, 2020

The 55th installment of the Top500 list saw strong activity in the leadership segment with four new systems in the top ten and a crowning achievement from the f 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

[email protected] Turns Its Massive Crowdsourced Computer Network Against COVID-19

March 16, 2020

For gamers, fighting against a global crisis is usually pure fantasy – but now, it’s looking more like a reality. As supercomputers around the world spin up Read more…

By Oliver Peckham

[email protected] Rallies a Legion of Computers Against the Coronavirus

March 24, 2020

Last week, we highlighted [email protected], a massive, crowdsourced computer network that has turned its resources against the coronavirus pandemic sweeping the globe – but [email protected] isn’t the only game in town. The internet is buzzing with crowdsourced computing... Read more…

By Oliver Peckham

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

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems waded deliberately into the then calmer quantum computing (QC) waters. Fast forward to March when Honeywell announced plans to introduce an ion trap-based quantum computer whose ‘performance’ would... Read more…

By John Russell

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

Global Supercomputing Is Mobilizing Against COVID-19

March 12, 2020

Tech has been taking some heavy losses from the coronavirus pandemic. Global supply chains have been disrupted, virtually every major tech conference taking place over the next few months has been canceled... Read more…

By Oliver Peckham

Leading Solution Providers

Contributors

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

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

‘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

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

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

March 19, 2020

As supercomputers around the world spin up to combat the coronavirus, the Texas Advanced Computing Center (TACC) is announcing results that may help to illumina Read more…

By Staff report

$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

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