PepBDB collected all the biological complex structures of peptide-mediated protein interactions with peptide lengths up to 50 residues in the Protein Data Bank. A valid PepBDB record is a peptide-protein complex where the peptide directly binds to at least one protein chain. PepBDB used the biological units when searching the complexes meeting the criteria. The pdb files were carefully processed to obtain cleaned peptide-protein complex structures and binding residues. The database presents extensive information about biological peptide-mediated protein interactions. PepBDB allows users to search the database by a variety of options including sequences and interactively visualize the peptide-protein complex structures and interactions. The database is updated monthly to include new data released in the PDB.