Protein-based drug carriers are promising candidates for efficient drug delivery among the available potential colloidal carrier systems, due to their low cytotoxicity, abundance, renewability, diverse functional groups and interactions, and high drug loading capacity, etc. In this study, molecular dynamics (MD) simulations are performed to study the mechanisms of 11S molecule of soy protein as drug delivery vehicle to attach allyl isothiocyanate (AITC) and doxorubicin (DOX) drugs. The intermolecular interactions between protein and drugs are investigated; and the loading capacities of the protein molecules are calculated and compared with experiments. It is found that, for the AITC system, both nonpolar and polar residues of protein have the ability to adsorb AITCs; particularly, the polar residues serve as the primary active sites for the stable attachment of the drug molecules through the electrostatic (dipole-dipole) interactions. For the DOX system, however, the main driving force become the π-π stacking (the van der Waals interactions) among the aromatic rings of DOX and protein. In addition to pristine protein, different denaturation processes are found to be able to increase the exposure of active sites, therefore, enhance the loading efficiency of the protein carriers.