Researchers will examine peptides, which play a critical role in stimulating the body's immune response to viral attack.
By understanding the structure and behaviour of the peptide, the research team hopes to pave the way for the design of multiple drugs capable of targeting the infection process.
"Our early results show that we can use computers to simulate which molecules can stop the HIV virus from infecting humans, allowing drug makers to more rapidly develop those drugs," said Jason Crain, at the University of Edinburgh's school of physics.
"This is a new approach to drug design. 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 University of Edinburgh installed Europe's first IBM Blue Gene supercomputer in 2004 in a bid to help lab experts and researchers throughout Britain tackle a range of scientific puzzles.
"By combining experimental research and the world's most powerful supercomputer we just might get much closer to that goal," said IBM researcher Glenn Martyna.