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Wednesday, March 7, 2007

International Grid battles Malaria

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[Excerpts from BSA]

From Sheffield to Singapore, International Grid Battles Malaria

Malaria kills more than one million people each year, most of them
young children living in Africa. Now physicists in the UK have shared
their computers with biologists from countries including France and
Korea in an effort to combat the disease. Using an international
computing Grid spanning 27 countries, scientists on the WISDOM project
analysed an average of 80,000 possible drug compounds against malaria
every hour. In total, the challenge processed over 140 million
compounds, with a UK physics Grid providing nearly half of the
computing hours used.

The computers are all part of EGEE (Enabling Grids for E-sciencE),
which brings together computing Grids from different countries and
disciplines. Up to 5000 computers were used simultaneously, generating a total of 2000 GB (2,000,000,000,000 bytes) of useful data.

Most of the UK's contribution came from GridPP, a computing Grid
funded by the Particle Physics and Astronomy Research Council and
built to process data from the world's largest particle physics
accelerator, due to be turned on later this year in Geneva. Professor
Tony Doyle, the GridPP Project Leader, explains, "Although our Grid
was built to analyse particle physics data, when we have spare
capacity we're able to share it with other scientists worldwide. In
this case, we're happy to have contributed more than two million hours
of computer time to help find drugs against malaria."

This challenge of the international WISDOM (World-wide In Silico
Docking On Malaria) initiative ran between 1 October and 31 January.
Its analysis of possible docking arrangements between drug compounds
and target proteins of the malaria parasite will greatly speed up the
search for drugs against malaria. WISDOM uses in silico docking, where
computers calculate the probability that molecules will dock with a
target protein. This lets researchers rule out the vast majority of
potential drugs, so they can concentrate on the most promising
compounds in laboratory tests. As well as speeding up the screening
process, this reduces the cost of developing new drugs to treat

"The impact of WISDOM goes much beyond malaria," declared Doman Kim,
Director of the Bioindustry and Technology Institute at Jeonnam
National University in Korea. "The method developed can be extended to
all diseases and this opens exciting industrial perspectives. Until
now, the search for new drugs in the academic sector was done at a
relatively small scale whereas the WISDOM approach allows a systematic
inquiry of all the potentially interesting molecules."

A second computing challenge targeting avian flu in April and May 2006
has significantly raised the interest of the biomedical research
community. Laboratories in France, Italy, Venezuela and South Africa
proposed targets for the second challenge against neglected diseases.
The WISDOM researchers plan a further data challenge on avian flu
later in 2007.

In addition to the computing power of the EGEE Grid (of which GridPP
is a part), AuverGrid, EELA, EUChinaGRID, EUMedGRID and South East
Asia Grid all provided additional resources. The Embrace and
BioinfoGRID projects are contributing to the development of a virtual,
in silico screening pipeline that will allow researchers to select,
for any given target protein, the most active molecules out of the
millions of compounds commercially available.

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