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Jared Adolf-Bryfogle; firstname.lastname@example.org; PI: Roland Dunbrack
Part of the RosettaAntibody and RosettaAntibodyDesign (RAbD) Framework
Runs the full Rosetta Antibody Design (RAbD) mover. Requires an AHo numbered antibody. Note that only the top design will move on in RosettaScripts. See the Rosetta Antibody Design (RAbD) Manual for more information. Note that the AntibodyDesignProtocol runs the
AntibodyDesignMover, but has a simpler interface. Any antibody design options discussed in the antibody design documentation but not set through the XML (as outlined in this document) can be set through the Command line.
Generally, one would want to do a simple run that optimizes the interface energy and uses cluster-based profiles for sequence design:
<AntibodyDesignMover seq_design_cdrs="(&string (ex: L1,L1,L3))" mc_optimize_dG="1"/>
If you want to explore different loop conformations of different CDRs, you can use the
graft_design_cdrs option to graft these on from the database and refine. You may use any combination of sequence and graft design CDRs. There are many more options, like being able to limit the length, or staying within the current cluster. In order to control these, you would pass a
cdr_instruction_file. See the full RAbD manual for more: RosettaAntibodyDesign#antibody-design-cdr-instruction-file
<AntibodyDesignMover graft_design_cdrs="(&string (ex: L1,L1,L3))" seq_design_cdrs="(&string (ex: L1,L1,L3))" mc_optimize_dG="1"/>
Autogenerated Tag Syntax Documentation:
Author: Jared Adolf-Bryfogle (email@example.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.
<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;)" 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;)" 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;)" />