We use the software specified by the organization whose work we are going to run on the grid. It's up to them. Typically the software is developed either in a university (Rosetta) or by the organization themselves (AutoDock). They're going to use whatever meets their scientific needs.

Interestingly enough, while Rosetta and AutoDock are certainly well known programs within their respecitve research circles, the vast exposure that World Community Grid gave these programs is far larger than they ever imagined. This has spurred development for both of the programs to make them better and more efficient. For example, the upcoming "Human Proteome Folding 2" project will use the next generation of Rosetta. Many of the changes and improvements to the software come directly as a result of running on World Community Grid.

So, not only are we doing decades of science in mere months, we are helping improve and tune these scientific programs to make the next generation of analysis even better, whether run on World Community Grid or not. So you see, World Community Grid's impact runs much deeper than just data being crunched.