Docking flexible peptides upon to a potential binding partner is performed with the Flexible Peptide Docking (FlexPepDock) framework of the Rosetta software suite1,2,3. Starting from a peptide sequence and an approximate location of the binding site, peptides can be simultaneously folded de novo and docked. The framework offers a refinement, ab initio and global docking protocol. The refinement protocol can be utilized to refine a coarse-grain model of the interaction, while ab initio additionally handles a peptide with no prior knowledge of its backbone conformation. The global docking protocol is designed for cases where not even the binding site is known. The FlexPepDock framework enables high-resolution peptide modeling and thus enables detailed structure-based studies of peptide-protein interactions.
More information on the FlexPepDock framework can be found at:
 Raveh, Barak, Nir London, and Ora Schueler‐Furman. "Sub‐angstrom modeling of complexes between flexible peptides and globular proteins." Proteins: Structure, Function, and Bioinformatics 78.9 (2010): 2029-2040
 Raveh, Barak, et al. "Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors." PloS one 6.4 (2011): e18934
 Alam, Nawsad, et al. "High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock." PLoS computational biology 13.12 (2017): e1005905