DesignByCavityProximity

This task operations scans the protein to identify intra-protein voids, and selects residues for design based on their proximity to the voids. Residues are scored by the metric (distance_to_cavity_center)/(volume_of_cavity) and the lowest scoring residues are selected for design.

<DesignByCavityProximity name="(&string)" region_shell="(8.0 &real)" regions_to_design="(1 &int)" repack_non_selected="(0 &bool)" />

region_shell: The radius of a sphere that surrounds the residue selected for mutation. All residues within this sphere will be set to design, and all residues outside of it will not be designed.
repack_non_selected: If set, residues outside of the design sphere will be repacked, otherwise they will be fixed.
regions_to_design: The number of residues (and regions based on the value of region_shell) to be selected for design.

Example The following example redesigns a sphere of 8 A radius centered at a residue near an intra-protein cavity. Residues outside of the sphere are fixed.

<TASKOPERATIONS>
    <DesignByCavityProximity name="des_cavity" region_shell="8.0" regions_to_design="1" repack_non_selected="0" />
</TASKOPERATIONS>
<MOVERS>
    <PackRotamersMover name="design" task_operations="des_cavity" />
</MOVERS>
<PROTOCOLS>
    <Add mover_name="design" />
</PROTOCOLS>

DesignByCavityProximity

DesignByCavityProximity

See Also