The growing availability of the high-throughput omics technologies has enabled construction of large-scale biological networks that map complex interactions among genes, proteins, metabolites, and transcripts. Among these, protein–protein interaction (PPI) networks are particularly significant for elucidating molecular mechanisms underlying cellular processes and disease progression. Topological analysis using graph-theoretical measures, such as centrality metrics, offers insights into the structural and functional organization of biological systems and aids in identifying key regulatory nodes and potential drug targets. This chapter presents an overview of widely used tools and platforms for PPI network analysis, focusing on software that support centrality-based characterization, network visualization, and functional annotation.