A key interaction in T-cell mediated Immunity involves cleaved protein fragments (peptides) binding to Major Histocompability Complexes (MHCs). The now peptide-MHC (pMHC) complex is transported to the surface of the cell, where it is scanned by the T-cell receptor, which recognizes self-peptides from non-self peptides stemming from infected/tumor cells. Identifying which peptides bind to MHCs is crucial for developing cancer immunotherapies. Recognizing the inherent structural characteristics in T-cell mediated interactions, we develop tools that perform structural modeling and structural analysis of pMHC complexes.