I am trying to use Rosetta dock and antibody design modules to design antibody in order to improve the affinity of the antibody to the antigen. Firstly I docked the antibody to the antigen. In this step I got 500 and antibody-antigen complex models and selected top 10 models based on the lowest I_sc energy. Then I ran AntibodyDesign using a command like the follow for each of the 10 complex models:
-s docking/ab_ag_0001.pdb \
-primary_cdrs H3 \
-graft_design_cdrs H3 \
-seq_design_cdrs H1 H2 \
-mc_total_weight .001 \
-mc_interface_weight .999 \
-nstruct 1 | tee design.log
By doing this I get 10 designed models and the corresponding antibody sequences. But how should I select the most possible model and the antibody sequence? The score items in the output score.sc file that may be relevent include:
Which score items should I use to choose the designed antibodies?
Besides, would it be helpful to including other options for running antibody_designer such as "-do_dock", "-use_epitope_constraints", "-paratope", etc.? And is it a routine to produce only one structure for antibody_designer?
With many thanks!