To demonstrate the improved performance of PepMapper over either MimoPro or Pep-3D-Search alone, we first present the results from MimoPro and Pep-3D-Search run separately and then the results from the combined operations. Table 2 presents the evaluation results from the two methods run separately. The performances of prediction from MimoPro and Pep-3D-Search varied in different test cases. MimoPro provided some good results on 2ADF_A, 3EZE_B, 1JRH_I, 1BJ1_H, 1N8Z_C and 1ZTX_E with sensitivity exceeding 0.8 and specificity higher than 0.6; meanwhile the worst results were observed in 1YY9_A, 2NY7_G, 2GRX_A, 1D4V_B, 3BT1_A and 1HX1_A with sensitivity approaching to 0. For the rest cases, the sensitivity of prediction was between 0.25 and 0.6 and the specificity is consistently higher than 0.8. Comparatively, Pep-3D-Search gave better results in 1HX1_A and 1D4V_B, in which MimoPro failed to predict any epitopic amino acids. However, Pep-3D-Search failed in 2ADF_A, 1EER_A and 1MQ8_B whereas MimoPro produced useful results. On average, MimoPro gives better results in terms of sensitivity (0.446) and precision (0.267), but slightly worse than Pep-3D-Search in specificity.