Exscalate Platform Addresses Zika Epidemic

April 11, 2019

April 11 — Powered by CINECA’s Marconi supercomputer, EXSCALATE (EXaSCale smArt pLatform Against paThogEns) is accelerating the search for new drugs, setting a new record: a “chemical library” of 500 billion molecules, up to 30 biological targets evaluated simultaneously, with a processing capacity of more than 3 million molecules a second and a screening cost for 1 billion molecules equivalent to 4,000 euro.

This performance clearly exceeds by far the current “state of the art” technology which is also the subject of a recent article in Nature (6 February 2019, https://www.nature.com/articles/s41586-019-0917-9) whereby a “chemical library” of 138 million molecules of a single target has been reached, with a processing capacity of less than 2 thousand molecules per second.

This result is the outcome of a public-private consortium, created within the European project ANTAREX – via a 3 million euro funding – within the H2020 Future and Emerging Technologies supercomputing program, which sees as pharmaceutical leader Dompé (an industrial partner for health applications) along with the Politecnico di Milano (the project coordinator and application acceleration partner) and CINECA (the technological partner that adapted the application to the Marconi supercomputer).

The EXSCALATE platform’s first test field is the epidemiological crisis caused by the Zika virus, which to date is still lacking effective treatment. In this case EXSCALATE has identified molecules potentially capable of inhibiting 5 of the 7 viral proteins: NS5, NS1, NS2B/NS3, NS3 and the membrane protein. The most promising molecules identified through the Exscalate platform are now undergoing biological testing.

The case study carried out on the Zika virus will be “open” to the international community and the results made public through the ANTAREX4ZIKA.eu website.

The idea of a platform capable of considerably accelerating the in-silico pharmaceutical research stems from almost ten years of investments by Dompé pharmaceuticals, through its Drug Discovery platform dedicated to the development of drugs through advanced in-silico methods. The starting point for the development of the central tool of the Exscalate platform was the structure-based virtual screening software by LiGen (Ligand Generator). LiGen is the result of an extensive collaboration between Dompé and the Italian supercomputing centre Cineca; the software was initially engineered to run in a native and effective manner on supercomputing architectures and was already one of the most competitive tools in the virtual screening software arena. Through the ANTAREX project, Dompé took the opportunity to incorporate the new technologies necessary for the transition to the era of exascale computing in LiGen. Thanks to the intelligent calculation techniques developed at the Politecnico di Milano, led by the Prof. Cristina Silvano and Prof. Gianluca Palermo group, and the close collaboration with an interdisciplinary group from CINECA and DOMPE’, it was possible to implement the LiGen software and take full advantage of the computing power of Marconi, one of the top 20 supercomputers in the world installed at CINECA.

“Thanks to this scientific collaboration, which has involved both public and private organizations, the aim is to make available to the research community a simulation system capable of supporting and accelerating the discovery of innovative therapies to fight pandemics such as the Zika virus,” comments Andrea Beccari, the EXSCALATE and Dompé’s Drug Discovery Platform manager. “Thanks to this work, it is now possible to optimize the ‘evaluation’ of a number of molecules never reached before and therefore to drastically reduce the virtual screening process on pharmacologically relevant targets in order to arrive at the identification of new active compounds.”

EXSCALATE can represent a model for scientific research and for the pharmaceutical industry: or rather, it can place the best European IT-engineering skills into a system with the most innovative pharmaceutical chemistry applied with the aim of making the most of Italian and European technological infrastructures. This opens up the possibility of reducing the path to important treatments for public health, while favouring the rapid availability of drug candidates that are evaluated in a very short time.

“Within the European project, where Exscalate was created,” adds Cristina Silvano of the Politecnico di Milano, coordinator of the ANTAREX project, “we had the idea of applying the concept of intelligent calculation in order to focus the computational effort on the data processing’s most promising points. This has made it possible to respond to the need to increase the number of molecules to be analyzed coming from the pharmaceutical world.” “Finding the best parameters on which to act within the application, configuring them appropriately for each type of processing, together with the use of approximate computation techniques,” underlines Gianluca Palermo, from the Politecnico di Milano, “have been one of the key points of the multi-disciplinary collaboration behind the development of EXSCALATE.”

“This project is placed within the more general framework of urgent computing, or rather the simulations required by national and international bodies in order to obtain operational responses within the least time possible,” adds Carlo Cavazzoni, HPC Cineca R&D Manager. “It will also soon benefit from further upgrading of the current European calculation infrastructure which, thanks to an investment of over 1 billion euro granted by the EuroHPC Joint Undertaking, will allow Europe to become one of the world’s largest supercomputing leaders.”


Source: Politecnico di Milano

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!

What’s New in HPC Research: Rabies, Smog, Robots & More

October 14, 2019

In this bimonthly feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here. Read more…

By Oliver Peckham

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ll get there at last month’s MIT-IBM Watson AI Lab’s AI Read more…

By John Russell

Summit Simulates Braking – on Mars

October 14, 2019

NASA is planning to send humans to Mars by the 2030s – and landing on the surface will be considerably trickier than landing a rover like Curiosity. To solve the problem, NASA researchers are using the world’s fastes Read more…

By Staff report

Chaminade University’s Immersion Program Builds Capacity for Data Science in Hawaii, Pacific Region

October 10, 2019

Kuleana is a uniquely Hawaiian value and practice which embodies responsibility to self, community, and the ‘aina' (land). At Chaminade University, a federally designated Native Hawaiian serving university in Hawai‘i Read more…

By Faith Singer-Villalobos

Trovares Drives Memory-Driven, Property Graph Analytics Strategy with HPE

October 10, 2019

Trovares, a high performance property graph analytics company, has partnered with HPE and its Superdome Flex memory-driven servers on a cybersecurity capability the companies say “routinely” runs near-time workloads on 24TB-capacity systems... Read more…

By Doug Black

AWS Solution Channel

Making High Performance Computing Affordable and Accessible for Small and Medium Businesses with HPC on AWS

High performance computing (HPC) brings a powerful set of tools to a broad range of industries, helping to drive innovation and boost revenue in finance, genomics, oil and gas extraction, and other fields. Read more…

HPE Extreme Performance Solutions

Intel FPGAs: More Than Just an Accelerator Card

FPGA (Field Programmable Gate Array) acceleration cards are not new, as they’ve been commercially available since 1984. Typically, the emphasis around FPGAs has centered on the fact that they’re programmable accelerators, and that they can truly offer workload specific hardware acceleration solutions without requiring custom silicon. Read more…

IBM Accelerated Insights

HPC in the Cloud: Avoid These Common Pitfalls

[Connect with LSF users and learn new skills in the IBM Spectrum LSF User Community.]

It seems that everyone is experimenting about cloud computing. Read more…

Intel, Lenovo Join Forces on HPC Cluster for Flatiron

October 9, 2019

An HPC cluster with deep learning techniques will be used to process petabytes of scientific data as part of workload-intensive projects spanning astrophysics to genomics. AI partners Intel and Lenovo said they are providing... Read more…

By George Leopold

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Summit Simulates Braking – on Mars

October 14, 2019

NASA is planning to send humans to Mars by the 2030s – and landing on the surface will be considerably trickier than landing a rover like Curiosity. To solve Read more…

By Staff report

Trovares Drives Memory-Driven, Property Graph Analytics Strategy with HPE

October 10, 2019

Trovares, a high performance property graph analytics company, has partnered with HPE and its Superdome Flex memory-driven servers on a cybersecurity capability the companies say “routinely” runs near-time workloads on 24TB-capacity systems... Read more…

By Doug Black

Intel, Lenovo Join Forces on HPC Cluster for Flatiron

October 9, 2019

An HPC cluster with deep learning techniques will be used to process petabytes of scientific data as part of workload-intensive projects spanning astrophysics to genomics. AI partners Intel and Lenovo said they are providing... Read more…

By George Leopold

Optimizing Offshore Wind Farms with Supercomputer Simulations

October 9, 2019

Offshore wind farms offer a number of benefits; many of the areas with the strongest winds are located offshore, and siting wind farms offshore ameliorates many of the land use concerns associated with onshore wind farms. Some estimates say that, if leveraged, offshore wind power... Read more…

By Oliver Peckham

Harvard Deploys Cannon, New Lenovo Water-Cooled HPC Cluster

October 9, 2019

Harvard's Faculty of Arts & Sciences Research Computing (FASRC) center announced a refresh of their primary HPC resource. The new cluster, called Cannon after the pioneering American astronomer Annie Jump Cannon, is supplied by Lenovo... Read more…

By Tiffany Trader

NSF Announces New AI Program; Plans $120M in Funding Next Year

October 8, 2019

As the saying goes, when you’re hot, you’re hot. Right now, AI is scalding. Today the National Science Foundation announced a new AI initiative – The National Artificial Intelligence Research Institutes program – with plans to invest about “$120 million in grants next year... Read more…

By Staff report

DOE Sets Sights on Accelerating AI (and other) Technology Transfer

October 3, 2019

For the past two days DOE leaders along with ~350 members from academia and industry gathered in Chicago to discuss AI development and the ways in which industr Read more…

By John Russell

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

Chinese Company Sugon Placed on US ‘Entity List’ After Strong Showing at International Supercomputing Conference

June 26, 2019

After more than a decade of advancing its supercomputing prowess, operating the world’s most powerful supercomputer from June 2013 to June 2018, China is keep Read more…

By Tiffany Trader

D-Wave’s Path to 5000 Qubits; Google’s Quantum Supremacy Claim

September 24, 2019

On the heels of IBM’s quantum news last week come two more quantum items. D-Wave Systems today announced the name of its forthcoming 5000-qubit system, Advantage (yes the name choice isn’t serendipity), at its user conference being held this week in Newport, RI. Read more…

By John Russell

A Behind-the-Scenes Look at the Hardware That Powered the Black Hole Image

June 24, 2019

Two months ago, the first-ever image of a black hole took the internet by storm. A team of scientists took years to produce and verify the striking image – an Read more…

By Oliver Peckham

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

Intel Confirms Retreat on Omni-Path

August 1, 2019

Intel Corp.’s plans to make a big splash in the network fabric market for linking HPC and other workloads has apparently belly-flopped. The chipmaker confirmed to us the outlines of an earlier report by the website CRN that it has jettisoned plans for a second-generation version of its Omni-Path interconnect... Read more…

By Staff report

Kubernetes, Containers and HPC

September 19, 2019

Software containers and Kubernetes are important tools for building, deploying, running and managing modern enterprise applications at scale and delivering enterprise software faster and more reliably to the end user — while using resources more efficiently and reducing costs. Read more…

By Daniel Gruber, Burak Yenier and Wolfgang Gentzsch, UberCloud

Intel Debuts Pohoiki Beach, Its 8M Neuron Neuromorphic Development System

July 17, 2019

Neuromorphic computing has received less fanfare of late than quantum computing whose mystery has captured public attention and which seems to have generated mo Read more…

By John Russell

Rise of NIH’s Biowulf Mirrors the Rise of Computational Biology

July 29, 2019

The story of NIH’s supercomputer Biowulf is fascinating, important, and in many ways representative of the transformation of life sciences and biomedical res Read more…

By John Russell

Quantum Bits: Neven’s Law (Who Asked for That), D-Wave’s Steady Push, IBM’s Li-O2- Simulation

July 3, 2019

Quantum computing’s (QC) many-faceted R&D train keeps slogging ahead and recently Japan is taking a leading role. Yesterday D-Wave Systems announced it ha Read more…

By John Russell

With the Help of HPC, Astronomers Prepare to Deflect a Real Asteroid

September 26, 2019

For years, NASA has been running simulations of asteroid impacts to understand the risks (and likelihoods) of asteroids colliding with Earth. Now, NASA and the European Space Agency (ESA) are preparing for the next, crucial step in planetary defense against asteroid impacts: physically deflecting a real asteroid. Read more…

By Oliver Peckham

ISC Keynote: Thomas Sterling’s Take on Whither HPC

June 20, 2019

Entertaining, insightful, and unafraid to launch the occasional verbal ICBM, HPC pioneer Thomas Sterling delivered his 16th annual closing keynote at ISC yesterday. He explored, among other things: exascale machinations; quantum’s bubbling money pot; Arm’s new HPC viability; Europe’s... Read more…

By John Russell

Argonne Team Makes Record Globus File Transfer

July 10, 2019

A team of scientists at Argonne National Laboratory has broken a data transfer record by moving a staggering 2.9 petabytes of data for a research project.  The data – from three large cosmological simulations – was generated and stored on the Summit supercomputer at the Oak Ridge Leadership Computing Facility (OLCF)... Read more…

By Oliver Peckham

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