Depp was trained on
over 1500 known (i.e. experimentally confirmed) protein phosphorylation sites.
The observation that amino acid composition, sequence complexity, hydrophobicity,
charge and other sequence attributes of regions adjacent to phosphorylation
sites are very similar to those of intrinsically disordered protein regions
suggests that disorder in and around the potential phosphorylation target site
is an important prerequisite for phosphorylation.
Thus, DEPP uses disorder information to improve the discrimination between
phosphorylation and non-phosphorylation sites. The accuracy of DEPP reaches 76.0
+/- 0.3%, 81.3 +/- 0.3% and 83.3 +/- 0.3% for serine, threonine and tyrosi
respectively.
Only residues with a prediction >0.5 are considered to be phosphorylated. The
score generally approximates the probability that the residue is phosphorylated.