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Autogenerated Tag Syntax Documentation:
Uses the same code underlying the ShapeComplementarity filter to calculates the Lawrence and Coleman shape complementarity of secondary structure elements of a protein with one another. Essentially, secondary structure elements (e.g. loops, helices) are cut from the protein and their shape complementarity is calculated against the rest of the protein. The protein is then returned to its state when the filter was called and the next secondary structure element is cut and computed. The value calculated is equal to sum( sc_i*a_i )/a_tot, where sc_i is the shape complementarity value of secondary structure element i with the rest of the protein, a_i is the area of interaction of secondary structure element i with the rest of the protein, and a_tot is the total intraprotein area of all secondary structure elements. Sheets are currently not supported. The secondary structure elements can optionally be specified using a blueprint file. For antibody-antigen interfaces, a value of 0.65-0.67 is typical, while complementarity among intra-protein secondary structure elements is typically higher, on the order of 0.7-0.8. This filter returns false if the overall shape complementarity value is below min_sc (set by the user), true otherwise.
<SSShapeComplementarity name="(&string;)" blueprint="(&string;)" secstruct="(&string;)" residue_selector="(&string;)" verbose="(false &bool;)" loops="(true &bool;)" helices="(true &bool;)" min_sc="(0.0 ℜ)" confidence="(1.0 ℜ)" />
The following example XML will create a SecondaryStructureShapeComplementarity filter which uses the secondary structure definitions in "input.blueprint" and computes the SC of all helices with the rest of the protein.
<FILTERS> <SSShapeComplementarity name="ss_sc" blueprint="input.blueprint" verbose="1" loops="0" helices="1" /> <FILTERS> <PROTOCOLS> <Add filter_name="ss_sc" /> </PROTOCOLS>