PCP is a sofware that searches for cliques in the modified network, and merge cliques to form clusters using a “partial clique merging” method. Experiments show that (1) the use of indirect interactions and topological weight to augment protein-protein interactions can be used to improve the precision of clusters predicted by various existing clustering algorithms; and (2) our complex-finding algorithm performs very well on interaction networks modified in this way. Since no other information except the original PPI network is used, the would be very useful for protein complex prediction, especially for prediction of novel protein complexes.
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J Bioinform Comput Biol. 2008 Jun;6(3):435-66.
Using indirect protein-protein interactions for protein complex prediction.
Chua HN, Ning K, Sung WK, Leong HW, Wong L.