FlexPepDock doesn’t predict peptide binding site. It models peptide once peptide is placed in the binding site.
We have developed a protocol which does binding site prediction. Here is the paper:
Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions.
Lavi A1, Ngan CH, Movshovitz-Attias D, Bohnuud T, Yueh C, Beglov D, Schueler-Furman O, Kozakov D.