Computational biology is an important, rapidly growing area of deep computing. The protein folding problem is one of the most intriguing problems - how does a protein form a three dimensional structure when it is placed in water? Modeling this process goes far beyond the capabilities of current supercomputers. I will discuss the problem as well as different solution approaches currently being tried. I will also discuss a project called Blue Gene which will build a petaflop scale supercomputer suitable for one approach to this problem within the next three years.