Cell-penetrating peptides comprising cloned epitopes that contribute to membrane transduction, DNA-binding and cell targeting functions are known to facilitate nucleic acid delivery. Using the ITASSER software, we predicted the 3-D structure of a well characterized and efficient transfecting cell-penetrating peptide, namely TAT-Mu and its derivative TAT-Mu-AF protein that harbors a targeting ligand, the HER2-binding affibody. Our model predicts TAT-Mu-AF fusion protein as primarily comprising α-helices. The affibody in TAT-Mu-AF is predicted as a 3-helical domain that is distinct from the TAT-Mu domain. Its positioning in three-dimensional structure is oriented in a manner that possibly favors interactions with receptor and facilitates transport to the target site. The linker region between TAT-Mu and the affibody is also predicted as a helix that is likely to stabilize the overall fold of the TAT-Mu-AF complex. Further, the evaluation of secondary structure of the designed TAT-Mu-AF fusion protein by circular dichroism is in support of our predictions.