In the post-genomic era,proteomics has achieved significant theoretical and practical advances with the devel-opment of high-throughput technologies.Especially the rapid accumulation of protein-protein interactions(PPIs)provides a foundation for constructing protein interaction networks(PINs),which can furnish a new perspective for understand-ing cellular organizations,processes,and functions at network level.In this paper,we present a comprehensive survey on three main characteristics of PINs:centrality,modularity,and dy-namics.1)Different centrality measures,which are used to cal-culate the importance of proteins,are summarized based on the structural characteristics of PINs or on the basis of its integrated biological information;2)Different modularity definitions and various clustering algorithms for predicting protein complexes or identifying functional modules are introduced;3)The dy-namics of proteins,PPIs and sub-networks are discussed,re-spectively.Finally,the main applications of PINs in the com-plex diseases are reviewed,and the challenges and future re-search directions are also discussed.