Protein Folding and the IBM BlueGene Supercomputer

Understanding how proteins fold is an important step in uncovering the mysteries of protein function. To date, the computational resources needed to simulate even the shortest and simplest protein folds have been astronomical. Simulation of larger and more complex folds has been prohibitively expensive. In 1999, IBM announced the start of an effort to build a supercomputer, the BlueGene, to be applied to biomolecular problems such as protein folding. This paper provides an overview of the problem of protein folding, a description of IBM’s BlueGene project, and what we may hope to gain once the machine is fully operational.