typedef subgraph< adjacency_list<vecS, vecS, undirectedS, Protein, PPI > > PPIGraph;
PPIGraph flyGraph;

gives error

invalid application of 'sizeof' to incomplete type 'boost::STATIC_ASSERTION_FAILURE<false>'

Does anyone know what the problem is?

No. You have to give substantially more information about your problem if anybody is going to help diagnose it. Compiler, operating system, line numbers, files, a little example of how you're using the class?
 
Andrew Sutton
andrew.n.sutton@gmail.com