University of Edinburgh uses supercomputer to tackle HIV virus

The University of Edinburgh and IBM's TJ Watson Research Centre have announced a five-year joint research project to use supercomputing simulations combined with lab experiments to speed the design of drugs aimed at inhibiting infection by the HIV virus

The project includes IBM's Blue Gene supercomputer, combined with new experimental characterisations aimed at targeting the infection process itself by designing inhibitors for the part of the virus responsible for allowing the virus' genetic material to enter the human cell. The new aspect of the collaboration is its attempt to design multiple inhibitors simultaneously and to thereby prevent the cagey virus from mutating and invalidating the drug therapy, as it does with single inhibitors.

"This is a new approach to drug design," said Jason Crain, of the University of Edinburgh's School of Physics and Divisional Head of Science at the National Physical Laboratory. "We are using sophisticated algorithms coupled with experimental techniques to design improved molecular therapies and we can capitalise on enormous computing power to do this efficiently and rationally."

The project is focused on how the human HIV-1 virus attaches to cells in the body and injects its genetic material. Researchers are examining a fragment of the surface protein of the virus - called a peptide - which is crucial in stimulating the body's immune response to viral attack. Understanding the structure and behaviour of the peptide will allow for multiple drugs to be designed simultaneously capable of targeting the infection process.

In 2004, the University of Edinburgh installed the first IBM Blue Gene supercomputer in Europe in an effort to help researchers throughout the UK tackle some of the most challenging puzzles in science. In partnership with IBM, this collaboration uses atomistic simulation methods and software run on IBM's massively parallel BlueGene/L supercomputer, in conjunction with high accuracy experimental techniques, to probe the properties of amino acids and small peptides - the building blocks of proteins - which are key to novel antiviral therapy based on the simultaneous development of multiple targets.

Further information: www.watson.ibm.com
www.ed.ac.uk

Image: A small segment of the HIV viral protein bound to a human antibody molecule, shown in yellow

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