The most widely used anti-cancer drug, cyclophosphamide (inset) acts by binding (cross-linking) two (guanine) bases of the DNA of a cancerous cell. Two chlorine atoms from the drug (green in the inset) are stripped off in the body and replaced by two nitrogen atoms (shown by arrows) of the DNA. This forms the bonding that prevents DNA replication, thus killing the cancerous cell. When broken down by the body, the side chain shown on the lower left of the inset is released, causing toxic side effects. Though this research required massive amounts of computation, calculations thousands of times more complex are needed to fully understand the activity of this drug.
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Atomic structure of a rationally-designed inhibitor bound to the active site of HIV protease (“ribbon” structure). The structure of the complex was determined by x-ray crystallographic analysis using a supercomputer networked to a high seed graphics workstation.