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A View from Brittany Sauser

IBM Fights HIV

The company is using its supercomputing prowess to augment experiments at the University of Edinburgh investigating the HIV infection process.

  • April 3, 2008

IBM’s T. J. Watson Research Center and the University of Edinburgh, in Scotland, hope that within five years they will be able to suggest new therapeutic strategies for inhibiting HIV infections. The company and the university are collaborating to study how the virus mutates: IBM’s supercomputer Blue Gene will perform simulations, while lab experiments are conducted at the university.

“The aim [of the project] is to develop new molecular medical techniques that will inhibit the fusion of the HIV virus to the target cells it affects,” says Jason Crain, a professor in the school of physics at the University of Edinburgh and the divisional head of science at the U.K.’s National Physical Laboratory. There is only one drug past phase III clinical trails that claims to prevent the initial assault on target cells, says Crain. Previous therapies have treated already infected cells.

“We want to understand more about the molecular processes that are involved in the viral fusion and the docking and binding processes,” says Crain. “Without the use of Blue Gene, we would not have the computer power to deploy such molecular-scale simulations.”

In order to harness the supercomputer’s power, IBM researchers are writing new algorithms to describe the molecules involved in the binding process at the atomic level. The new software will run on massively parallel machines so that the researchers can more effectively simulate the structures of molecules in different solutions and how a particular molecule will react in the presence of the virus, says Glen Martyna, the lead IBM researcher for the project.

Combining the simulations with lab experiments will improve the researchers’ interpretation of experimental data and validate the computational models, says Crain. “The end goal is to accelerate the discovery process,” he says.

IBM and the university have been loosely collaborating for the past five years, looking at biophysical simulations on a relatively small scale–single amino acids or fragments of viral peptides and proteins. “The results are encouraging, and now we are moving that project into a seriously biomechanical domain,” says Crain.

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