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Selects residues for design that have the highest value of residue centrality. Centrality is determined by the intra-protein interaction network. Residues are defined as interacting and receive an edge in the network if they have atoms that are <= 4 angstroms apart. The residue centrality is the average of the average shortest path from each node to all other nodes, and can be used to identify residues that are structurally or functionally important.
This task operation is stochastic to allow for variation in design regions. Residues are selected by this task operation as follows. First, all residues are ranked in order of network centrality. Next, the first residue is selected based on a random number generator. The first residue in the list (the one with highest centrality) has a 50% probability of being selected, the second residue has 25% probability, and so on. If regions_to_design is > 1, additional residues are selected using the same process, except with previously chosen residues removed from consideration.
<DesignByResidueCentrality name="(&string)" region_shell="(8.0 &real)" regions_to_design="(1 &int)" repack_non_selected="(0 &bool)" />
Example The following example redesigns a sphere of 8 A radius centered at a residue of high centrality. Residues outside of the sphere are fixed.
<TASKOPERATIONS>
<DesignByResidueCentrality name="des_by_centrality" region_shell="8.0" regions_to_design="1" repack_non_selected="0" />
</TASKOPERATIONS>
<MOVERS>
<PackRotamersMover name="design" task_operations="des_by_centrality" />
</MOVERS>
<PROTOCOLS>
<Add mover_name="design" />
</PROTOCOLS>