Table 2

Binding site prediction error for two domain-oriented methods and PIPE-Sites (this work)

Species

Pairs originally in validation set

Method

Pairs with available predictions

Error (average DM)

Yeast

265

DPEA

32

0.718

Yeast

265

DOMINE

144

0.363

Yeast

265

PIPE-Sites (this work)

174

0.218

Human

423

DPEA

2

N/A *

Human

423

DOMINE

266

0.306

Human

423

PIPE-Sites (this work)

363

0.246

DPEA [12] is a standalone statistical inference method, while DOMINE [25] is a database combining several experimental and computational domain-domain interaction sources. We used a consensus approach to combine the 13 constituent data sources of DOMINE to arrive at a single binding site prediction. Error is expressed as average distance between the predicted site and lab-confirmed site, averaged over all pairs. * Due to the small sample size (only 2 available predictions), it was impossible to calculate a statistically significant average DM for DPEA predictions.

Amos-Binks et al. BMC Bioinformatics 2011 12:225   doi:10.1186/1471-2105-12-225