I am an researcher in computer science. I am interesting in the alignment problem of PPI networks of difference species. I know a PPI network is a graph in its nature. I want to know whether there are any structural characteristics or constraints of a protein-protein interaction network (such as, a certain kind of protein can only have certain kinds of interactions with other proteins, a certain kind of protein can appears in a PPI network at most certain times, and any thing like this). If a PPI network does't satisfy these structural characteristics or constraints, then people can know that this PPI network is not a valid one.
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I have changed the problem's description according to your comments. Thanks. – Saturn Nov 30 '15 at 00:50