scripting_documentation/RosettaScripts/xsd/mover_AntibodyCDRGrafter

Autogenerated Tag Syntax Documentation:

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) Graft CDR loops from one structure to another, optionally optimize CDRs and neighbor CDRs of the grafted one. Results in 100 percent loop closure if using both graft graft movers (where peptide bond geometries of both ends are checked relative to ideal values).

References and author information for the AntibodyCDRGrafter mover:

AntibodyCDRGrafter 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.

CCDEndsGraftMover 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.

AnchoredGraftMover Mover's citation(s): Lewis SM, and Kuhlman BA. (2011). Anchored Design of Protein-Protein Interfaces. PLoS ONE 6(6): e20872. doi: doi:10.1371/journal.pone.0020872.

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.

<AntibodyCDRGrafter name="(&string;)" cdrs="(&string;)" cdr="(&string;)"
        cdr_definition="(&string;)" input_ab_scheme="(&string;)"
        donor_structure_from_pdb="(&string;)"
        donor_structure_from_spm="(&string;)" reference_name="(&string;)"
        use_secondary_graft_mover="(false &bool;)" scorefxn="(&string;)"
        nter_overhang="(3 &non_negative_integer;)"
        cter_overhang="(3 &non_negative_integer;)"
        stop_after_closure="(true &bool;)" optimize_cdrs="(false &bool;)"
        optimize_cdr4_if_neighbor="(true &bool;)" dihedral_cst_wt="(2.0 &real;)" />

cdrs: String specifying CDRs to graft
cdr: String specifying CDR to graft
cdr_definition: String defining CDRs
input_ab_scheme: Sets the antibody numbering scheme. Must also specify cdr_definition when using this option
donor_structure_from_pdb: Path to the structure used for the graft. Either use donor_structure_from_pdb or donor_structure_from_spm. One of these is required.
donor_structure_from_spm: Takes donor structure from the SavePoseMover. Either use donor_structure_from_pdb or donor_structure_from_spm (one is required )
reference_name: Name of reference pose to use (Use the SavePoseMover to create a reference pose)
use_secondary_graft_mover: Should we use the secondary graft mover if the graft is not closed using the first?
scorefxn: Name of score function to use
nter_overhang: Number of extra residues on the Nter side of the CDR to use for grafting
cter_overhang: Number of extra residues on the Cter side of the CDR to use for grafting
stop_after_closure: Should we stop after graft closure?
optimize_cdrs: Should we optimize grafted and neighbor CDRs using dihedral constrained relax?
optimize_cdr4_if_neighbor: Optimize CDR4 if a neighbor CDR is grafted
dihedral_cst_wt: Weight of dihedral constraints used during optimization

scripting_documentation/RosettaScripts/xsd/mover_AntibodyCDRGrafter_type