Grid Search for H5N1 Cure

[frogfish]

Grid searches for avian flu cure

The computers are speeding up lab work to combat avian flu

A cure for bird flu is being sought by computers that usually search for the fundamental elements of matter.

In April, the UK grid of computers that crunches data from particle physics experiments was used by scientists to study the avian H5N1 virus.

The grid simulated the reactions of 300,000 chemical compounds to find which ones might combat the bug.

The project aims to make grids available to scientists that need to call on lots of computer power.

Drug trials

Computer grids tie together ranks of low-powered machines to create a virtual supercomputer.

For this project, computers at 11 British universities and research labs were used to search through candidate compounds that might help combat H5N1.

Before now, the grid of computers was organised as the GridPP project, which harnessed machines to comb through the data generated by physics experiments.

"GridPP has been developed to help answer questions about the conditions in the Universe just after the Big Bang," said Professor Keith Mason, head of the Particle Physics and Astronomy Research Council (PParc).

"But the same resources and techniques can be exploited by other sciences with a more direct benefit to society."

A grid creates a virtual supercomputer to analyse data

During April, 2000 machines from the GridPP project were used, and they generated more than 600 gigabytes of data. On a single computer, it would take about 100 years to carry out the same amount of analysis.

The machines were looking for molecules that bind to the virus to inhibit its activity.

Specifically, the compounds need to interrupt the working of the neuraminidase enzyme, subtype N1, found on the surface of the virus. It is this enzyme that helps the virus infect more cells.

The data from the number crunching effort is now being analysed to see which candidate compounds performed best. Without the ability to simulate, researchers would have to go through a much longer trial-and-error process in the laboratory to find useful compounds.

The results have been passed to the consortium of Asian and European laboratories engaged in the search for a way to combat H5N1.

"This will free up medicinal chemists' time to better respond to instant, large-scale threats," said Ying-Ta Wu, biologist at the Genomics Research Center of the Academia Sinica in Taipei.

"Moreover, we can concentrate our biological assays in the laboratory on the most promising components, the ones we expect to have the greatest impact."

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Hopefully they find one in time...