Aflatoxin M1 (AFM1) and seven structural analogs were used to investigate the correlation between antibody binding and the conformational and electronic properties of these molecules. Mice were immunized with AFM1-BSA and hybridomas secreting anti-AFM1 antibodies were isolated and characterized. The cross-reactivities of seven structurally similar aflatoxins were determined by competition enzyme-linked immunosorbent assay (cELISA). In an effort to correlate antibody binding with three-dimensional properties of the analogs, all of the aflatoxins (and the immunogen) were modeled and global energy minima were determined using molecular, mechanical and quantum mechanical methods. The results demonstrate that, for these molecules, loss of optimum structure and introduction of steric hindrance in the portion of the molecule that would fit into the antibody binding site are more important to binding than simply loss of a determinant group. Molecular computational techniques can give reasons for the wide variation in IC50 values observed between structural analogs and can be used as a tool for determining which conformational and electronic properties of molecules are most important for antibody binding.