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Primeur weekly 2016-05-09

Focus

NIST's Robert Bohn and Oxford University's David Wallom expand on Cloud standards and the Cloud landscape ...

With trust, openness and empowerment, there is a bright future for Cloud computing, according to Microsoft's Elena Bonfiglioli ...

Quantum computing

IBM makes quantum computing available on IBM Cloud to accelerate innovation ...

Quantum logical operations realized with single photons ...

Focus on Europe

Celebrating HPC and research at University College London ...

Still time to save on ISC 2016 registration - Register by May 11 ...

Current status of the Flemish supercomputer ...

Middleware

Bright Computing names Bill Griffin as Chief Financial Officer ...

Hardware

Invitation to participate in HPC Site Census study ...

CSRA to deliver high capacity connectivity to support education priorities in Alabama ...

Cray reports first quarter 2016 financial results ...

Applications

SDSC researchers publish book on using GPU accelerators for nanosciences ...

Movidius announces deep learning accelerator and Fathom software framework ...

GPU-powered systems take top spot and set new record in Student Supercomputer Competition ...

Fine-tuning forecasts of nighttime storms on the plains ...

Sudden collapse: Supercomputing spotlight on gels ...

BSC and IrsiCaixa create bioinformatics method to predict the effectiveness of antiretroviral drugs with different HIV mutations ...

University of Wyoming faculty have until May 22 to apply for supercomputer use ...

Webinar on performance tuning and optimization of GROMACS ...

IBM and SK Holdings C&C Alliance brings Watson and the cognitive era to South Korea ...

BSC and IrsiCaixa create bioinformatics method to predict the effectiveness of antiretroviral drugs with different HIV mutations


9 May 2016 Barcelona - The effectiveness of antiretroviral drugs used to treat HIV (human immunodeficiency virus) is frequently affected by the virus' ability to develop genetic mutations. Barcelona Supercomputing Center (BSC) and IrsiCaixa, the Catalan AIDS Research Institute, have developed a bioinformatics method to predict the effect of each mutation on the resistance of the virus to such drugs. An article published in theJournal of Chemical Information and Modelingexplains how this method has effectively predicted the resistance of the virus with genetic mutations in the HIV-1 protease, a protein which is essential for the replication of the virus, to the drugs amprenavir and darunavir. The method could easily be applied to other drugs and proteins.

Currently, information obtained from other patients is used to predict the effects of HIV mutations on drug effectiveness. Built cumulatively through clinical experience, this knowledge is useful but has limitations. For example, it is unable to provide answers when the virus develops a mutation which hasn't previously been recorded. The method created by BSC and IrsiCaixa overcomes these drawbacks by providing predictions based on the characteristics of each genetic mutation and on the changes which the mutation produces in the virus' proteins which act as targets for the drugs.

The BSC-IrsiCaixa method combines HIV DNA sequencing, identification of genetic mutations, computational protein modelling and the simulation of drugs binding with the proteins of the virus. The entire bioinformatics analysis can be performed in fewer than 24 hours on relatively small-scale computing equipment available to any laboratory. One of the main features of the system is the use of PELE, a piece of software developed at BSC to predict how drugs will interact with their targets, which has been shown to have competitive advantages over commercially available software.

BSC has created an automatic platform, available for free via the web, on which researchers can enter a patient's HIV-1 PR protease genomic sequence and predict the effectiveness of prescribing the drugs amprenavir and darunavir. For the moment, these are the only predictions available, pending advances in research on the effect of HIV mutations on other proteins within the virus and interactions with other antiretroviral drugs.

BSC researcher Victor Guallar, who appears as principal investigator in the article published in theJournal of Chemical Information and Modelingand is the lead developer of PELE, explains that "this system is one of the first tangible steps in the area of what will eventually be personalised medicine, where treatment will be decided following genetic analysis of the causes of the disease in each patient and of which drug would be most effective in each individual case".

"In this study we demonstrate how to connect routine clinical diagnosis of HIV-1 with structural computer modelling. This is a multidisciplinary proof of concept which overcomes the limitations of current practice when deciding antiretroviral treatment and which, in addition, allows new drugs to be designed more quickly", added IrsiCaixa researcher Marc Noguera-Julian, who participated in the study.

The article is titled " Computational Prediction of HIV-1 Resistance to Protease Inhibitors ".

Source: Barcelona Supercomputing Center - BSC

Back to Table of contents

Primeur weekly 2016-05-09

Focus

NIST's Robert Bohn and Oxford University's David Wallom expand on Cloud standards and the Cloud landscape ...

With trust, openness and empowerment, there is a bright future for Cloud computing, according to Microsoft's Elena Bonfiglioli ...

Quantum computing

IBM makes quantum computing available on IBM Cloud to accelerate innovation ...

Quantum logical operations realized with single photons ...

Focus on Europe

Celebrating HPC and research at University College London ...

Still time to save on ISC 2016 registration - Register by May 11 ...

Current status of the Flemish supercomputer ...

Middleware

Bright Computing names Bill Griffin as Chief Financial Officer ...

Hardware

Invitation to participate in HPC Site Census study ...

CSRA to deliver high capacity connectivity to support education priorities in Alabama ...

Cray reports first quarter 2016 financial results ...

Applications

SDSC researchers publish book on using GPU accelerators for nanosciences ...

Movidius announces deep learning accelerator and Fathom software framework ...

GPU-powered systems take top spot and set new record in Student Supercomputer Competition ...

Fine-tuning forecasts of nighttime storms on the plains ...

Sudden collapse: Supercomputing spotlight on gels ...

BSC and IrsiCaixa create bioinformatics method to predict the effectiveness of antiretroviral drugs with different HIV mutations ...

University of Wyoming faculty have until May 22 to apply for supercomputer use ...

Webinar on performance tuning and optimization of GROMACS ...

IBM and SK Holdings C&C Alliance brings Watson and the cognitive era to South Korea ...