I have read some papers about the use of genetic algorithms in searching
the conformation space of protein structure. These involve the work of
Carlos Lucasius and Gerrit Kateman at the University of Nijmegen, the
Netherlands. Although they do not mention any specialized hardware, this
seems (to a naive chemist) to be a suitable problem for it. Let me know
if this is of any use to you. Carlos is taking a postdoc position in our
lab this fall, I imagine he would be interested in your work.