Reply To: Modeling phosphate ion binding site in protein.

[Anonymous]

By “run the protocol” I mean dock the known structures with the ligand docking application, in the same way you’re docking your unknown structure. The thought is, if Rosetta does well on the known structures there is a reasonable chance it’ll do well for similar unknown structures. Conversely, if you can’t get good results with a known structure, you’re unlikely to get good results with a similar unknown structure.

The ligand docking application is intended for fixed sequence problems. The amino acid sequence of the protein you put in is the amino acid sequence of the protein you get out. If you want to change the sequence to improve affinity, you’ll probably want to use the enzyme design application. (http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/app_enzyme_design.html — while it’s called “enzyme design”, it also works for designing ligand binding proteins.) Internally, it’s much the same as the ligand docking application, but with extra features to allow for design.