Supercomputers Help Decode RNA Structure

July 13, 2017

ARGONNE, Ill., July 13, 2017 — A cure for cancer, HIV and other stubborn diseases has evaded the brightest minds for generations. But with supercomputers – computing systems that can calculate, analyze and visualize extremely large amounts of data – researchers are gaining a leg up in the fight for better treatments and cures.

Researchers at the National Cancer Institute (NCI) are using supercomputers at the U.S. Department of Energy’s (DOE) Argonne National Laboratory to advance disease studies by enhancing our understanding of RNA, biological polymers that are fundamentally involved in health and disease.

“Since the biologically active form of RNA is a 3-D structure, going from understanding the primary sequence and the two-dimensional layout of an RNA to understanding the 3-D form is a big stepping-stone that gives us a lot of useful information about biological functions, …”

In collaboration with staff from the Argonne Leadership Computing Facility (ALCF), researchers have perfected a technique that accurately computes the 3-D structure of RNA sequences. This method, which relies on a computer program known as RS3D and Mira – the ninth fastest supercomputer in the world – gives researchers studying cancer and other diseases structural insights about relevant RNAs that can be used to advance computer-assisted drug design and development.

RNA not only functions as a DNA interpretation messenger for protein fabrication, but also plays a multifaceted role in regulating gene expression – such as when, where and how efficiently a gene is expressed. For this reason, researchers are actively seeking to understand the functions of novel RNA sequences. And in order to get a complete picture, they need to know the biologically active forms of RNA, which are reflected in the complex 3-D structures that RNA sequences fold into after they’re created.

“We already know the basic chemical groups for RNA and how they’re composed, but what we don’t know is what conformational structures they take,” said Wei Jiang, a researcher at the Argonne Leadership Computing Facility who is one of the computational leads in the project.

“Getting the real functional structure, which is the 3-D structure, is very difficult to do experimentally, because the RNA polymer is too flexible,” he said. “This is why we rely on computational simulation. Simulations can be used to explore hundreds or thousands of possible conformational states that would eventually lead us to the most likely 3-D structure.”

The computer program RS3D was developed by a National Cancer Institute research team, led by researcher Yun-Xing Wang and postdoctoral fellow Yuba Bhandari, and optimized by ALCF researchers to run on Mira; Jiang played a central role in scaling the RS3D code to run on a large fraction of Mira, which improved its performance significantly.

As an input, RS3D uses known RNA sequence information and experimental data from small angle X-ray scattering, a technique that provides important structural information, such as particle size and shape, based on the scattering pattern that is generated when X-ray beams are applied to a target sample. With these inputs, RS3D outputs a low-resolution 3-D image of the topological structure of RNA that provides the most likely folding patterns.

“Since the biologically active form of RNA is a 3-D structure, going from understanding the primary sequence and the two-dimensional layout of an RNA to understanding the 3-D form is a big stepping-stone that gives us a lot of useful information about biological functions,” said Bhandari, one of the leaders of the project. “Understanding the structural basis provides a foundation for further investigating molecular interactions and biological pathways in various diseases.”

The researchers validated their technique by using it to compute the 3-D structure of 18 RNA polymers whose structures are known. These select RNAs fold into a wide variety of structures that represent common folding architectures. Additionally, researchers used R3SD along with experimental data recorded at the synchrotron light source at Argonne, the Advanced Photon Source, to compute the structure of adenine riboswitch, an RNA structure known to regulate gene expression.

“One of the unique and advantageous features of this technique is the fact that it’s fully automated, meaning it does not require the user to input an initial 3-D structural template to work. This sets it apart from other methods that perform similar calculations,” Bhandari said. “This helps us eliminate any potential limitations or biases that could be introduced through a template, and make the whole approach easier to apply.”

The researchers are now in the process of publishing their technique; the source code will be made available to researchers thereafter. A brief summary of their computational work, presented in an article titled “Modeling RNA topological structures using small angle X-ray scattering,” is published in Methods.

This work is funded by the Intramural Research Programs of the National Cancer Institute. This work employed resources at the Argonne Leadership Computing Facility and the Advanced Photon Source, both DOE Office of Science User Facilities. Experimental data for adenine riboswitch RNA was recorded at Sector 12 of the Advanced Photon Source. Computing time was awarded through the ALCF’s Director’s Discretionary Program.

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 the Office of Science website.


Source: Joan Koka, ANL

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!

New Exascale System for Earth Simulation Introduced

April 23, 2018

After four years of development, the Energy Exascale Earth System Model (E3SM) will be unveiled today and released to the broader scientific community this month. The E3SM project is supported by the Department of Energy Read more…

By Staff

RSC Reports 500Tflops, Hot Water Cooled System Deployed at JINR

April 18, 2018

RSC, developer of supercomputers and advanced HPC systems based in Russia, today reported deployment of “the world's first 100% ‘hot water’ liquid cooled supercomputer” at Joint Institute for Nuclear Research (JI Read more…

By Staff

New Device Spots Quantum Particle ‘Fingerprint’

April 18, 2018

Majorana particles have been observed by university researchers employing a device consisting of layers of magnetic insulators on a superconducting material. The advance opens the door to controlling the elusive particle Read more…

By George Leopold

HPE Extreme Performance Solutions

Hybrid HPC is Speeding Time to Insight and Revolutionizing Medicine

High performance computing (HPC) is a key driver of success in many verticals today, and health and life science industries are extensively leveraging these capabilities. Read more…

Cray Rolls Out AMD-Based CS500; More to Follow?

April 18, 2018

Cray was the latest OEM to bring AMD back into the fold with introduction today of a CS500 option based on AMD’s Epyc processor line. The move follows Cray’s introduction of an ARM-based system (XC-50) last November. Read more…

By John Russell

Cray Rolls Out AMD-Based CS500; More to Follow?

April 18, 2018

Cray was the latest OEM to bring AMD back into the fold with introduction today of a CS500 option based on AMD’s Epyc processor line. The move follows Cray’ Read more…

By John Russell

IBM: Software Ecosystem for OpenPOWER is Ready for Prime Time

April 16, 2018

With key pieces of the IBM/OpenPOWER versus Intel/x86 gambit settling into place – e.g., the arrival of Power9 chips and Power9-based systems, hyperscaler sup Read more…

By John Russell

US Plans $1.8 Billion Spend on DOE Exascale Supercomputing

April 11, 2018

On Monday, the United States Department of Energy announced its intention to procure up to three exascale supercomputers at a cost of up to $1.8 billion with th Read more…

By Tiffany Trader

Cloud-Readiness and Looking Beyond Application Scaling

April 11, 2018

There are two aspects to consider when determining if an application is suitable for running in the cloud. The first, which we will discuss here under the title Read more…

By Chris Downing

Transitioning from Big Data to Discovery: Data Management as a Keystone Analytics Strategy

April 9, 2018

The past 10-15 years has seen a stark rise in the density, size, and diversity of scientific data being generated in every scientific discipline in the world. Key among the sciences has been the explosion of laboratory technologies that generate large amounts of data in life-sciences and healthcare research. Large amounts of data are now being stored in very large storage name spaces, with little to no organization and a general unease about how to approach analyzing it. Read more…

By Ari Berman, BioTeam, Inc.

IBM Expands Quantum Computing Network

April 5, 2018

IBM is positioning itself as a first mover in establishing the era of commercial quantum computing. The company believes in order for quantum to work, taming qu Read more…

By Tiffany Trader

FY18 Budget & CORAL-2 – Exascale USA Continues to Move Ahead

April 2, 2018

It was not pretty. However, despite some twists and turns, the federal government’s Fiscal Year 2018 (FY18) budget is complete and ended with some very positi Read more…

By Alex R. Larzelere

Nvidia Ups Hardware Game with 16-GPU DGX-2 Server and 18-Port NVSwitch

March 27, 2018

Nvidia unveiled a raft of new products from its annual technology conference in San Jose today, and despite not offering up a new chip architecture, there were still a few surprises in store for HPC hardware aficionados. Read more…

By Tiffany Trader

Inventor Claims to Have Solved Floating Point Error Problem

January 17, 2018

"The decades-old floating point error problem has been solved," proclaims a press release from inventor Alan Jorgensen. The computer scientist has filed for and Read more…

By Tiffany Trader

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown Read more…

By Tiffany Trader

Russian Nuclear Engineers Caught Cryptomining on Lab Supercomputer

February 12, 2018

Nuclear scientists working at the All-Russian Research Institute of Experimental Physics (RFNC-VNIIEF) have been arrested for using lab supercomputing resources to mine crypto-currency, according to a report in Russia’s Interfax News Agency. Read more…

By Tiffany Trader

How the Cloud Is Falling Short for HPC

March 15, 2018

The last couple of years have seen cloud computing gradually build some legitimacy within the HPC world, but still the HPC industry lies far behind enterprise I Read more…

By Chris Downing

Chip Flaws ‘Meltdown’ and ‘Spectre’ Loom Large

January 4, 2018

The HPC and wider tech community have been abuzz this week over the discovery of critical design flaws that impact virtually all contemporary microprocessors. T Read more…

By Tiffany Trader

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Fast Forward: Five HPC Predictions for 2018

December 21, 2017

What’s on your list of high (and low) lights for 2017? Volta 100’s arrival on the heels of the P100? Appearance, albeit late in the year, of IBM’s Power9? Read more…

By John Russell

Leading Solution Providers

Deep Learning at 15 PFlops Enables Training for Extreme Weather Identification at Scale

March 19, 2018

Petaflop per second deep learning training performance on the NERSC (National Energy Research Scientific Computing Center) Cori supercomputer has given climate Read more…

By Rob Farber

Lenovo Unveils Warm Water Cooled ThinkSystem SD650 in Rampup to LRZ Install

February 22, 2018

This week Lenovo took the wraps off the ThinkSystem SD650 high-density server with third-generation direct water cooling technology developed in tandem with par Read more…

By Tiffany Trader

AI Cloud Competition Heats Up: Google’s TPUs, Amazon Building AI Chip

February 12, 2018

Competition in the white hot AI (and public cloud) market pits Google against Amazon this week, with Google offering AI hardware on its cloud platform intended Read more…

By Doug Black

HPC and AI – Two Communities Same Future

January 25, 2018

According to Al Gara (Intel Fellow, Data Center Group), high performance computing and artificial intelligence will increasingly intertwine as we transition to Read more…

By Rob Farber

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Te Read more…

By John Russell

US Plans $1.8 Billion Spend on DOE Exascale Supercomputing

April 11, 2018

On Monday, the United States Department of Energy announced its intention to procure up to three exascale supercomputers at a cost of up to $1.8 billion with th Read more…

By Tiffany Trader

Momentum Builds for US Exascale

January 9, 2018

2018 looks to be a great year for the U.S. exascale program. The last several months of 2017 revealed a number of important developments that help put the U.S. Read more…

By Alex R. Larzelere

Google Chases Quantum Supremacy with 72-Qubit Processor

March 7, 2018

Google pulled ahead of the pack this week in the race toward "quantum supremacy," with the introduction of a new 72-qubit quantum processor called Bristlecone. Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Share This