Autogenerated Tag Syntax Documentation:
Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) Main mover of RosettaAntibodyDesign (RAbD). One can set seq_design_cdrs if only sequence designing CDRs (which will use CDR cluster-profiles by default) and/or graft_design_cdrs to control which CDRs graft-designed through integrated antibody database sampling(if any). A cdr instruction file can be set to further limit these options or set only specific lengths or clusters to be designed. The interface will be analyzed at the end of the protocol and information added to the scorefile. light_chain must be set either in the tag or on the cmd-line. Please see the RAbD Manual for more information.
References and author information for the AntibodyDesignMover mover:
AntibodyDesignMover Mover's citation(s): Adolf-Bryfogle J, Kalyuzhniy O, Kubitz M, Weitzner BD, Hu X, Adachi Y, Schief WR, and Dunbrack Jr RL Jr. (2018). RosettaAntibodyDesign (RAbD): A general framework for computational antibody design. PLoS Comput Biol 14(4):e1006112. doi: 10.1371/journal.pcbi.1006112.
<AntibodyDesignMover name="(&string;)" min_scorefxn="(&string;)"
atom_pair_cst_weight="(ℜ)" dihedral_cst_weight="(ℜ)"
global_atom_pair_cst_scoring="(&bool;)" scorefxn="(&string;)"
global_dihedral_cst_scoring="(&bool;)" light_chain="(&string;)"
seq_design_cdrs="(&string;)" graft_design_cdrs="(&string;)"
mintype="(&string;)" instruction_file="(&string;)"
mc_optimize_dG="(false &bool;)" mc_interface_weight="(1.0 ℜ)"
mc_total_weight="(0.0 ℜ)" do_dock="(&bool;)"
dock_first_cycles="(2 &positive_integer;)"
dock_second_cycles="(2 &positive_integer;)" use_epitope_csts="(&bool;)"
epitope_residues="(&string;)" paratope_cdrs="(&string;)"
random_start="(&bool;)"
design_protocol="(EVEN_CLUSTER_MC &ABdesign_protocols;)"
primary_cdrs="(&string;)" dock_cycles="(&non_negative_integer;)"
interface_dis="(ℜ)" neighbor_dis="(ℜ)"
outer_cycles="(&non_negative_integer;)"
relax_cycles="(&non_negative_integer;)"
inner_cycles="(&non_negative_integer;)"
mutate_framework_for_cluster="(&bool;)" outer_kt="(ℜ)"
inner_kt="(ℜ)" top_designs="(&non_negative_integer;)"
run_AIM="(&bool;)" remove_antigen="(&bool;)" />