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Primeur weekly 2012-12-10

The Cloud

Bull awarded for best Private Cloud project ...

Bull launches a new private Cloud data protection service ...

Bull extends its Le cloud by Bull offering, to help organisations reap the full benefit of the Cloud ...

Drag-and-Drop DNA: Novel technique aiding development of new cancer drugs ...

Galaxy on Cloud ...

IBM expands the power of social business with new Cloud and mobile advances ...

Oracle unveils Cloud and consolidation capabilities for Oracle SPARC SuperCluster ...

Desktop Grids

Call for Proposals for Open PhD Competition in Extreme Citizen Science ...

Crucial step in AIDS virus maturation simulated for first time ...

EuroFlash

SMB Engys buys hosted server cluster ...

HP harnesses the power of Big Data with new information optimization solutions ...

HP extends Converged Cloud Portfolio for hybrid delivery environments ...

HP redefines storage simplicity with single architecture for enterprises of all sizes ...

Sogeti consolidates client delivery centre infrastructure seeking business growth with IBM PureSystems ...

University of Manchester is celebrating supercomputing 50 years on ...

projectiondesign F32 projectors visualize the future for Petrobras Research Centres ...

Bismuth provides perfect dance partners for quantum computing qubits ...

USFlash

BP to build U.S. facility to house largest commercial research supercomputer in the world ...

Eurocom ships world's first 8-Core Intel Xeon E5-2690 based 12lbs supercomputer laptop ...

HP acknowledges global mission-critical computing innovators ...

Nextra Teleservices calls for IBM PureSystems over HP to deliver new high-speed broadband services in India ...

University of Kentucky takes academic supercomputing to next level ...

NCAR Officials to address supercomputer allocation use in 2013 ...

Interactive One connects with Oracle Database Appliance to meet high-traffic demands ...

Raritan announces first industry standard 802.11 Wi-Fi solution for intelligent power and environment ...

Grant creates science demilitarized zone at San Diego State University ...

Crucial step in AIDS virus maturation simulated for first time

4 Dec 2012 Barcelona - Bioinformaticians at IMIM - Hospital del Mar Medical Research Institute - and UPF - Pompeu Fabra University - have used molecular simulation techniques to explain a specific step in the maturation of the HIV virions, i.e., how newly formed inert virus particles become infectious, which is essential in understanding how the virus replicates. These results, which have been published in the latest edition ofPNAS, could be crucial to the design of future antiretrovirals.

HIV virions mature and become infectious as a result of the action of a protein called HIV protease. This protein acts like a pair of scissors, cutting the long chain of connected proteins that form HIV into individual proteins that will form the infectious structure of new virions. According to the researchers of the IMIM-UPF computational biophysics group: "One of the most intriguing aspects of the whole HIV maturation process is how free HIV protease, i.e. the 'scissors protein', appears for the first time, since it is also initially part of the long poly-protein chains that make up new HIV virions."

Using ACEMD, a software for molecular simulations and a technology known as GPUGRID.net, Gianni De Fabritiis' group has demonstrated that the first "scissors proteins" can cut themselves out from within the middle of these poly-protein chains. They do this by binding one of their connected ends (the N-terminus) to their own active site and then cutting the chemical bond that connects them to the rest of the chain. This is the initial step of the whole HIV maturation process. If the HIV protease can be stopped during the maturation process, it will prevent viral particles, or virions, from reaching maturity and, therefore, from becoming infectious.

This work was performed using GPUGRID.net, a voluntary distributed computing platform that harnesses the processing power of thousands of NVIDIA GPU accelerators from household computers made available by the public for research purposes. It's akin to accessing a virtual supercomputer. One of the benefits of GPU acceleration is that it provides computing power that is around 10 times higher than that generated by computers based on CPUs alone. It reduces research costs accordingly by providing a level computational power that previously was only available on dedicated, multi-million dollar supercomputers.

Researchers use this computing power to process large numbers of data and generate highly complex molecular simulations. In this specific case, thousands of computer simulations have been carried out, each for hundreds of nanoseconds (billionths of a second) for a total of almost a millisecond.

According to researchers, this discovery in the HIV maturation process provides an alternative approach in the design of future pharmaceutical products based on the use of these new molecular mechanisms. For now, this work provides a greater understanding of a crucial step in the life cycle of HIV, a virus that directly attacks and weakens the human immune system, making it vulnerable to a wide range of infections, and which affects millions of people around the world.

The paper titled "Kinetic characterization of the critical step in HIV-1 protease maturation" is written by S Kashif Sadiq, Frank Noe and Gianni De Fabritiis and appears inPNAS, DOI:10.1073/pnas.1210983109 at http://www.pnas.org/content/early/2012/11/21/1210983109.abstract?sid=9e8d7340-4d4c-4fa5-85a2-c68194eff067
Source: Insittut Municipal d'Investigacio Medica - Hospital del Mar

Back to Table of contents

Primeur weekly 2012-12-10

The Cloud

Bull awarded for best Private Cloud project ...

Bull launches a new private Cloud data protection service ...

Bull extends its Le cloud by Bull offering, to help organisations reap the full benefit of the Cloud ...

Drag-and-Drop DNA: Novel technique aiding development of new cancer drugs ...

Galaxy on Cloud ...

IBM expands the power of social business with new Cloud and mobile advances ...

Oracle unveils Cloud and consolidation capabilities for Oracle SPARC SuperCluster ...

Desktop Grids

Call for Proposals for Open PhD Competition in Extreme Citizen Science ...

Crucial step in AIDS virus maturation simulated for first time ...

EuroFlash

SMB Engys buys hosted server cluster ...

HP harnesses the power of Big Data with new information optimization solutions ...

HP extends Converged Cloud Portfolio for hybrid delivery environments ...

HP redefines storage simplicity with single architecture for enterprises of all sizes ...

Sogeti consolidates client delivery centre infrastructure seeking business growth with IBM PureSystems ...

University of Manchester is celebrating supercomputing 50 years on ...

projectiondesign F32 projectors visualize the future for Petrobras Research Centres ...

Bismuth provides perfect dance partners for quantum computing qubits ...

USFlash

BP to build U.S. facility to house largest commercial research supercomputer in the world ...

Eurocom ships world's first 8-Core Intel Xeon E5-2690 based 12lbs supercomputer laptop ...

HP acknowledges global mission-critical computing innovators ...

Nextra Teleservices calls for IBM PureSystems over HP to deliver new high-speed broadband services in India ...

University of Kentucky takes academic supercomputing to next level ...

NCAR Officials to address supercomputer allocation use in 2013 ...

Interactive One connects with Oracle Database Appliance to meet high-traffic demands ...

Raritan announces first industry standard 802.11 Wi-Fi solution for intelligent power and environment ...

Grant creates science demilitarized zone at San Diego State University ...