The protamine amino acids involved with the binding to the aptamer were Arg9, Ser29, Arg 24, Cys30, Thr32, Arg33, Met37. The interactions were mainly due to the highly positive nature of the protamine protein. Due to its high specificity for HER2, the HB5 aptamer performs better than the control aptamer, enabling precision drug delivery to breast cancer cells that overexpress HER2. Compared to the non-specific control aptamer, the therapeutic efficacy is significantly improved, and off-target effects are reduced. Similarly, the HB5 aptamer demonstrated a better binding orientation concerning the HER2 receptor in our computational analysis. The HB5 aptamer attaches vertically to the HER2 receptor, whereas the control aptamer binds horizontally, as shown in Figure . Both HB5 and control aptamer sequences were obtained by Liang et al. Vertical binding is preferred over horizontal binding for optimal nanovehicle attachment. This orientation enables more efficient cell-nanovehicle interaction. We did not model the ATP binding and aptamer/drug release mechanisms since they are computationally expensive.