It should be emphasized the necessity of experimental validation for potential researchers, because no ranking method may help if not associated with verification in the experiment. In an initial attempt, we applied the conventional consensus scoring method to re-rank the score list and experimental test through BACE-1 FRET assay, no inhibitor was found. However, when we applied the PCA scoring method and experimental test through BACE-1 FRET assay, a remarkable 10% hit rate was achieved. On this basis, we summed up some experience as followed: when virtual screening of a new chemical database, the potential researchers usually do not know which kind of individual scoring function work best for the target protein, furthermore, for consensus scoring protocol, they are uncertain which kind of scoring functions should be used to combine for getting the best enrichment rates. Once trapped in this dilemma, the researchers could use PCA scoring protocol to re-rank the results from the virtual screening, a prominent advantage of application of PCA scoring protocol can summarize most of the information from the original scoring functions and improve the enrichment rate, which has been proved to be robust and reliable in the present study.