Peptide is traditionally recognized as an important kind of biologically active substance, which involves in various physiological processes associated with the growth and development of organism. In recent years, however, since it was found that peptide plays a central role in cell signaling and could be exploited as therapeutic drugs targeting protein-protein interaction networks, researchers have redirected their interest to peptide-related topics. In particular, rapidly increasing efforts have been addressed on the use of computational and theoretical methods to investigate the physicochemical properties and biological implications underlying peptide recognition and interaction with protein. Here, we engage the theme “computational peptidology” to cover the field where the methods, strategies and protocols of computational chemistry and bioinformatics are employed to study peptides and peptide mimics. A systematic discussion is also addressed on the database configuration, function inference, molecular docking, dynamics simulation, structure analysis, design and modification, and systems biology of peptides. Through this perspective, we lay our emphasis on protein-peptide recognition and binding which are the basis of peptide-mediated protein interactions and peptidic drug discovery. We also rise the potential applications of computational peptidology in exploring and designing new peptide-based nanomaterials and biological surfactants. Contents 1 Introduction
2 The branches of computational peptidology
2.1 Peptide database
2.2 Peptide function prediction
2.3 Peptide docking
2.4 Peptide dynamics simulation
2.5 Peptide structure analysis
2.6 Peptide design and modification
2.7 Peptide systems biology
3 Conclusions and outlook