Peptide-protein interactions are ubiquitous in the celland form an important part of the interactome.Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. Here, we present a new fullyblindflexible peptide-protein docking protocol, pepATTRACT, which combines a rapid coarse-grained global peptide docking search of the entireprotein surface with a two-stage atomistic flexible refinement. Global unbound-unbound docking yielded near-native models for 70% of the docking cases when testing the protocol on the largest benchmark of peptide-protein complexes availableto date. This performance is similar tothat of state-of-the-art local docking protocols that rely on information about the binding site. Upon restricting the search to the peptide binding region, the resulting pepATTRACT-local approach outperformed existing methods. Docking scripts for pepATTRACT and pepATTRACT-local can be generated via a web interface at www.attract.ph.tum.de/peptide.html.