FlexPepDock Server

Rosetta FlexPepDock is a high-resolution peptide docking (refinement) protocol, implemented within the Rosetta framework. The input for this server is a PDB file of a complex between a protein receptor (first chain) and an estimated conformation for a peptide (second chain). FlexPepDock was shown to be able to accurately refine the peptide structure starting from up to 5.5A RMSD of the native conformation, allowing full flexibility to the peptide and side-chain flexibility to the receptor.

FunHunt Server

FunHunt is a classifier of correct protein-protein complex orientations. The input to FunHunt are two possible orientations of a complex. A local docking run is performed on the two complexes using RosettaDock. FunHunt then uses features gathered from these docking runs - representing the local energy landscapes of the orientations, and chooses the near-native orientation among both (assuming that one of the orientations is the near native one).