I wanna dock all 20 Individual residues against the target protein surface using RosettaDock and find the most important residue based on the affinity, shape complementary and binding scores. I'd like to tell rosetta to dock these residue against an specific area on the protein. I read an article published by Prof. Baker ''Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin, http://science.sciencemag.org/content/332/6031/816.full" which did this kind of docking.
Can you help me and give me helpful clues?
I'm not entirely sure, but I believe that they used the standard protein-protein docking protocol, but instead of two full-sized proteins they used one full-sized protein and one single residue "protein". I haven't tried it myself, but from what I understand, that should work*.
If you need help getting started with protein-protein docking, please see the Rosetta tutorials (https://www.rosettacommons.org/demos/latest/Home#tutorials) or ask additional questions here, if something isn't clear.
*) You may have issues with the docking protocol forming interactions with the backbone of the single residue partner. But you should be able to manually filter out those docked conformations as a post-processing step.