Both MimoPro and Pep-3D-Search failed in 1YY9_A, 2GRX_A, 1EER_A, and 3EZE_B. Consequently, PepMapper failed as well. We think that this failure could be attributed to a number of factors, including the quality of the experimental data and the complexity of the predicting tasks. For instance, we found that the mimotope set used for predicting the epitopic region of 2GRX_A is screened against the whole complementary protein rather than the restricted region of the two interacting proteins. Therefore it is reasonable to suppose that there may be multiple regions on the surface of the target antigen to which the mimotope can bind. As a result, the mimotopes may bind to the regions that are different from the preferable region.