Grid Computing Efforts Fight Avian Flu

Several major grid computing systems are applying their combined power to find effective candidates against a common research target in the most prevalent and harmful type of avian flu.

Over the last few months, a number of major international grid computing collaborations have been working to uncover more effective treatments for avian flu. Scientists are focusing on a particular research target in the strain of avian flu known as H5N1.

In April in the United States, The Rothberg Institute for Childhood diseases released the avian influenza target for H5N1 to the distributed computing project Drug Design and Optimization Lab, or D2OL. This information allows the D2OL software to model target proteins identified from the avian flu and then to simulate the binding of drug molecules with these targets to identify promising combinations that can potentially inhibit important disease pathways. The process is like searching through a collection of keys (drug candidates) to find the one that will fit a specific lock (target protein).

D2OL was already working to discover potential drug candidates against Anthrax, smallpox, Ebola, SARS and other infectious diseases. The grid computing effort has examined over 1 million potential treatment candidates and continues to proceed at the rate of more than 30,000 candidates a day.

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The project claims to be the first to use computational methods to deploy targets against these major infectious diseases. The research community is growing rapidly and currently comprises nearly 80,000 volunteers and their computers in 93 countries. As with some other grids, it works through the download of a free software application that contributes idle computer time to research.

Of all avian flu viruses that have infected humans, Avian Influenza A, or H5N1, has been found to be the most prevalent and harmful to human health. It is, therefore, the most likely of the avian flu viruses to mutate sufficiently to facilitate person-to-person infection, and the world continues to monitor avian flu hotbeds in Asia and Europe for the potential nucleus of a worldwide H5N1 pandemic. The first avian flu target released for the D2OL project is the H5N1 neuraminidase, which aids in the pathology and spread of the disease.

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Over the last month, another major grid effort harnessing computing resources in Europe also started work on the same H5N1 avian flu target. The project harnessed three existing European grid infrastructures, including Enabling Grids for E-sciencE (EGEE), an academic project bringing together the scientific computing power of over 90 research institutions in more than 30 countries. Funded by the European Commission, the EGEE grid consists of over 30,000 CPUs available to users 24 hours a day, seven days a week. The system is able to simultaneously maintain 10,000 concurrent jobs on average.

A collaboration of Asian and European laboratories is using this international grid to analyze 300,000 possible drug components against the Asian flu virus. Two thousand computers were used during April—the equivalent of 100 years on a single computer. More than 60,000 output files with a data volume of 600GB were created. Potential drug compounds against the avian flu are now being identified and ranked.

"The grid is useful for any kind of research that needs lots of computing power. In this case, its greatly speeded up a step in the search for drugs against avian flu," said Professor Tony Doyle, project leader for the United Kingdom particle physics grid, which contributes computing power from 11 universities.

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