This application in Rosetta3 was created and documented by David Johnson, et al.
This application takes in a PDB file of a protein complex and Robetta ddg prediction output and suggests optimal target residues for pocket optimization with the goal of directly inhibiting the protein-protein interaction. It does so by identifying how much ddg would be contained in the PocketGrid derived from every pair of interface residues. The best target residue pairs will be those whose PocketGriod containts the most ddg, implying the most likely location for an inhibitor to inhibit the interaction.
Johnson DK and Karanicolas J. Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations. PLoS Comput Biol. 2015;11(2):e1004081
Sample command
pocket_suggest_target_residues_by_ddg.linuxgccrelease -database ~/Rosetta/main/database -in:file:s complex.pdb -ddg_list ddg.txt -target_chain_list Apocket_suggest_target_residues_by_ddg options
General Rosetta Options
-database Path to rosetta databases
-in:file:s Input pdb file(s)
Other Mandatory Options
-ddg_list Text file of ddg output from Robetta server
-target_chain_list List of chains of the protein on which pocket optimization will be performed