The increase in the amount of available protein-protein interaction (PPI) data enables us to develop computational methods for protein complex predictions. A protein complex is a group of proteins that interact with each other at the same time and place. The protein complex generally corresponds to a cluster in PPI network (PPIN). However, clusters correspond not only to protein complexes but also to sets of proteins that interact dynamically with each other. As a result, conventional graph-theoretic clustering methods that disregard interaction dynamics show high false positive rates in protein complex predictions.