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Peptides have been used as flavors for decades, however, their tasting mechanism remains not entirely clear. In the present work, 10 kokumi peptides identified in yeast extracts were selected as ligands. Their binding mechanism to calcium-sensitive receptors (CaSR) were investigated at molecular level by using molecular docking and molecular dynamics simulations. The results showed that all kokumi peptides could bind to CaSR to form complexes, of which γ-Glu-Cys-Gly (GSH), γ-Glu-Leu (EL) and γ-Glu-Tyr (EY) being the top 3 peptides with higher affinity. Arg66, Ser147 and Ala168 may be the active sites of CaSR and interact with CaSR through hydrogen bonds; the different kokumi peptides and CaSR mainly rely on hydrogen bonding, electrostatic interaction and hydrophobic interaction to bind each other. This study provides a theoretical reference for the interaction between kokumi peptides and their receptors.