I feel I should point out that the Gates Foundation is no Microsoft. And that a grant from the foundation to participate in a global team of scientists on AIDS research should not imply any association, or participation from Microsoft.

The source code for Rosetta and Fold.it is not available to the public. But there are license agreements available for acedemic researchers. And if your goal was to port it, I would guess a license for that would be permitted as well...

but you have to keep in mind that Dr. Baker knows how Rosetta works, and he's already posted that the memory requirements to run Rosetta exceed what is supported on alternate platforms. And so another generation of such alternative platforms would be required before a port could begin.