What's the goal - what are you trying to infer? I don't know what you mean by "preferential attachment, duplication-mutation-complementation".
What we are trying to do is infer the evolutionary mechanisms by which organisms evolve increasingly complex systems of interacting proteins. A protein interaction network is a map of the organism's proteins and their interactions in the form of a graph: we represent each protein with a node, and draw an edge between two proteins if they can form a complex.
One of the first observations made about protein networks is that the degree distributions of their graphs seem to obey a power law: there are few nodes which have a huge number of interaction partners ...
There must be quite a few undergrad/graduate/post-doc/???-level researchers on LessWrong. I'm interested in hearing about your work. I'll post about myself in the comments.