Protein kinases are key drug targets for several diseases. However, despite large efforts, the development of drugs that are specific for these kinases has been a great challenge. The discovery that protein-protein interactions can be mediated by small linear sequences has invigorated the bioinformatics field and there are increasing efforts to create computer programs that identify and characterize linear sequences responsible for protein-protein interactions. The development of peptides as modulators of target protein activity is facilitated by in silico approaches. There are numerous applications for peptide modulators of protein-protein interactions and peptide modulators of kinase activity. Peptide modulators may be used either as tools to elucidate specific signaling pathways, as drug leads, or as drugs themselves. In the present review we will discuss the development of such peptide modulators and some of their applications.