The MHC Epitope energy (mhc_epitope) alogrithm (https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/MHCEpitopeEnergy) is for deimmunization of epitopes. However I cannot understand how to use it.
I used the pdb file 2b3p.pdb and the score controlling script in the introduction webpage as the inputs and run the following command:
rosetta_scripts.default.linuxgccrelease -s 2b3p.pdb -parser:protocol epitope.xml
The content of the "epitope.xml" is:
<ScoreFunction name="ref_deimm" weights="ref2015.wts">
<Reweight scoretype="mhc_epitope" weight="1"/>
I got two files as the output: a "score.sc" file and a "2b3p_0001.pdb" The score.sc file gives various energy terms, but none of them is related to MHC-epitope interaction energy (such as IC50, etc.). And the 2b3p_0001.pdb is exactly the same with the input structure.
As I understand, a deimmunization alogrithm can first predict all epitopes restricted by various MHC alleles in a protein and give the predicted IC50 of these epitopes, and then introduce mutaions in these epitopes so as to reduce the IC50 of the native epitopes. Could anyone tell me how to realize these functions with ROSETTA?
I will appreciate any help!