. 2012 Nov 29;7(11):e50300. doi: 10.1371/journal.pone.0050300

Table 4. Performance comparison of PROSPER with PoPS and SitePrediction based on independent test datasets extracted from recent proteomics profiling studies and a recent update of the MEROPS database.

Protease	Merops ID	Percentage of correctly predicted known cleavage sites (%)
		PoPS	SitePrediction	PROSPER
Caspase-3 ^a	C14.003	92.7	45.6	83.6
Matrix metallopeptidase-2 ^b	M10.003	17.6	3.9	29.4
Granzyme B (human) ^a	S01.010	47.8	-^c	76.9
Granzyme B (mouse) ^a	S01.136	65.1	-	77.4

Substrate datasets extracted from a recent update of the MEROPS database [34], [35];

Substrate dataset extracted from experimental data derived from N-terminal positional proteomics [20];

“-” denotes that the prediction result for this protease family is not available for this tool.

Note that these data are only available for a few proteases, including caspase-3, MMP-2, granzyme B (human) and granzyme B (mouse). The accuracy or sensitivity was calculated as the percentage of the known cleavage sites that were correctly predicted.