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Primeur weekly 2017-02-13

Focus

Funding agencies and academia need to rethink reward structure for computational tool developers to tackle big scientific challenges ...

OpenAire to support more technical e-Infrastructures with Open Research Data guidelines, publication and training ...

Exascale supercomputing

ISC High Performance keynote forecasts future role of HPC in weather and climage prediction ...

Crowd computing

Towards equal access to digital coins ...

Quantum computing

Large groups of photons on demand - an equivalent of photonic 'integrated circuit' ...

Protecting quantum computing networks against hacking threats ...

Sorting machine for atoms ...

Focus on Europe

HPC-Europa3 provides access to European HPC systems ...

Peter the Great Saint Petersburg Polytechnic University is first university to introduce computational computer code for Airbus ...

Middleware

Introducing Hazelcast Jet: a new lightweight, distributed data processing engine ...

Bright Computing announces strategic alliance with Curtiss-Wright ...

Hardware

NVIDIA powers new class of supercomputing workstations with breakthrough capabilities for design and engineering ...

Van Andel research institute optimises HPC pipeline to drive research discoveries and new drug therapies with end-to-end DDN solution ...

CoolIT Systems issued U.S. patent for modular heat-transfer solutions ...

ORNL researchers break data transfer efficiency record ...

Cray reports 2016 full year and fourth quarter financial results ...

Supermicro deploys 30,000+ MicroBlade servers to enable one of the world's highest Efficiency (1.06 PUE) data centres ...

Mellanox ships more than 100,000 cables for next generation 100 Gb/s networks ...

UMass Amherst boosts deep learning research with powerful new GPU cluster ...

Oak Ridge National Laboratory enhances data integrity and accessibility with Active Archive Solutions ...

Applications

ANSYS spurs pervasive engineering simulation with release 18 ...

Computing sciences students: Get your team together for the SC17 Student Cluster Competition in Denver ...

Latest Allinea update advances code optimization across platforms ...

Con Edison selects C3 IoT for Big Data and predictive analytics platform and applications ...

New algorithms may revolutionize drug discoveries - and our understanding of life ...

When data's deep, dark places need to be illuminated ...

Computer trained to predict which AML patients will go into remission and which will relapse ...

The Cloud

Cycle Computing collaborates with ANSYS on its Enterprise Cloud HPC offering ...

IBM launches "Digital - Nation Africa" and invests $70 million to bring digital skills to Africa with free, Watson-powered skills platform for 25 million people ...

New algorithms may revolutionize drug discoveries - and our understanding of life

According to University of Toronto PhD student Ali Punjani, the ability to determine the 3D structures of protein is critical in understanding how they work and how they will respond to drug therapies. Photo by Ken Jones.6 Feb 2017 Toronto - A new set of machine learning algorithms developed by University of Toronto researchers that can generate 3D structures of tiny protein molecules may revolutionize the development of drug therapies for a range of diseases, from Alzheimer's to cancer.

"Designing successful drugs is like solving a puzzle", stated University of Toronto PhD student Ali Punjani, who helped develop the algorithms. "Without knowing the three-dimensional shape of a protein, it would be like trying to solve that puzzle with a blindfold on."

The ability to determine the 3D atomic structure of protein molecules is critical in understanding how they work and how they will respond to drug therapies, noted Ali Punjani.

Drugs work by binding to a specific protein molecule and changing its 3D shape, altering the way it works once inside the body. The ideal drug is designed in a shape that will only bind to a specific protein or proteins involved in a disease while eliminating side effects that occur when drugs bind to other proteins in the body.

This new set of algorithms reconstructs 3D structures of protein molecules using microscopic images. Since proteins are tiny - even smaller than a wavelength of light - they can't be seen directly without using sophisticated techniques like electron cryomicroscopy (cryo-EM). This new method is revolutionizing the way scientists can discover 3D protein structures, allowing the study of many proteins that simply could not be studied in the past.

Cryo-EM is unique because it uses high-power microscopes to take tens of thousands of low-resolution images of a frozen protein sample from different positions. The computational problem is to then piece together the correct high-resolution 3D structure from the low-resolution 2D images.

"Our approach solves some of the major problems in terms of speed and number of structures you can determine", stated Professor David Fleet, chair of the Computer and Mathematical Sciences Department at University of Toronto Scarborough and Ali Punjani's PhD supervisor.

The algorithms, which were co-developed by David Fleet's former Post-Doctoral Fellow Marcus Brubaker, now an Assistant Professor at York University, could significantly aid in the development of new drugs because they provide a faster, more efficient means at arriving at the correct protein structure.

"Existing techniques take several days or even weeks to generate a 3D structure on a cluster of computers", stated Marcus Brubaker. "Our approach can make it possible in minutes on a single computer."

Ali Punjani added that existing techniques often generate incorrect structures unless the user provides an accurate guess of the molecule being studied. What's novel about their approach is that it eliminates the need for prior knowledge about the protein molecule being studied.

"We hope this will allow discoveries to happen at a ground-breaking pace in structural biology", stated Ali Punjani. "The ultimate goal is that it will directly lead to new drug candidates for diseases, and a much deeper understanding of how life works at the atomic level."

The research, which included a collaboration with University of Toronto Professor John Rubinstein, a Canada Research Chair in Electron Cryomicroscopy, received funding from the Natural Sciences and Engineering Research Council of Canada (NSERC). It's also been published in the current edition of the journal Nature Methods .

Meanwhile, the team's start-up, Structura Biotechnology Inc., has developed the algorithms into a new cryo-EM platform called cryoSPARC that is already being used in labs across North America. The start-up has received funding and support from University of Toronto's Innovations and Partnership's Office (IPO) through the Connaught Innovation Award, University of Toronto's Early Stage Technologies (UTEST) programme, the Ontario Centres of Excellence (OCE), and FedDev Ontario's Investing in Commercialization Partnerships programme with York University.

Source: University of Toronto

Back to Table of contents

Primeur weekly 2017-02-13

Focus

Funding agencies and academia need to rethink reward structure for computational tool developers to tackle big scientific challenges ...

OpenAire to support more technical e-Infrastructures with Open Research Data guidelines, publication and training ...

Exascale supercomputing

ISC High Performance keynote forecasts future role of HPC in weather and climage prediction ...

Crowd computing

Towards equal access to digital coins ...

Quantum computing

Large groups of photons on demand - an equivalent of photonic 'integrated circuit' ...

Protecting quantum computing networks against hacking threats ...

Sorting machine for atoms ...

Focus on Europe

HPC-Europa3 provides access to European HPC systems ...

Peter the Great Saint Petersburg Polytechnic University is first university to introduce computational computer code for Airbus ...

Middleware

Introducing Hazelcast Jet: a new lightweight, distributed data processing engine ...

Bright Computing announces strategic alliance with Curtiss-Wright ...

Hardware

NVIDIA powers new class of supercomputing workstations with breakthrough capabilities for design and engineering ...

Van Andel research institute optimises HPC pipeline to drive research discoveries and new drug therapies with end-to-end DDN solution ...

CoolIT Systems issued U.S. patent for modular heat-transfer solutions ...

ORNL researchers break data transfer efficiency record ...

Cray reports 2016 full year and fourth quarter financial results ...

Supermicro deploys 30,000+ MicroBlade servers to enable one of the world's highest Efficiency (1.06 PUE) data centres ...

Mellanox ships more than 100,000 cables for next generation 100 Gb/s networks ...

UMass Amherst boosts deep learning research with powerful new GPU cluster ...

Oak Ridge National Laboratory enhances data integrity and accessibility with Active Archive Solutions ...

Applications

ANSYS spurs pervasive engineering simulation with release 18 ...

Computing sciences students: Get your team together for the SC17 Student Cluster Competition in Denver ...

Latest Allinea update advances code optimization across platforms ...

Con Edison selects C3 IoT for Big Data and predictive analytics platform and applications ...

New algorithms may revolutionize drug discoveries - and our understanding of life ...

When data's deep, dark places need to be illuminated ...

Computer trained to predict which AML patients will go into remission and which will relapse ...

The Cloud

Cycle Computing collaborates with ANSYS on its Enterprise Cloud HPC offering ...

IBM launches "Digital - Nation Africa" and invests $70 million to bring digital skills to Africa with free, Watson-powered skills platform for 25 million people ...