Abstract: Provided are methods of identifying inhibitors of ?-secretase that employ modified ?-secretase substrates. The modified ?-secretase substrates have ?-secretase cleavage sites that are altered from wild type. The amino acid sequences of the altered ?-secretase cleavage sites contain different amino acids in at least one of the positions P2-P1-P1?-P2? of the ?-secretase cleavage site. Many of the modified ?-secretase substrates are more efficient substrates for ?-secretase than are corresponding substrates having wild-type sequences, that is, these modified substrates are more susceptible to enzymatic breakdown by ?-secretase. Recombinant polynucleotide molecules encoding the modified ?-secretase substrates are provided. Antibodies that recognize cleavage products of the modified ?-secretase substrates are provided. Stable cell lines expressing the modified ?-secretase substrates are provided. Transgenic animals expressing the modified ?-secretase substrates are provided.