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SSShapeComplementarity (SecondaryStructureShapeComplementarity)

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 &real;)" confidence="(1.0 &real;)" />
• blueprint: If specified, the given blueprint file will be used to assign secondary structure. If not specified, DSSP will be used.blueprint and secstruct tags are mutually exclusive
• secstruct: blueprint and secstruct tags are mutually exclusive
• residue_selector: . The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.
• verbose: If set, verbose output will be generated by the ShapeComplementarity calculator
• loops: If set, loops will be included in the calculations. Otherwise, they will be skipped.
• helices: If set, helices will be included in the calculations. Otherwise, they will be skipped.
• min_sc: The filter fails if the calculated overall shape complementarity is below this value. Set to 0.0 (always passing) by default.
• confidence: Probability that the pose will be filtered out if it does not pass this Filter

Example

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>
</PROTOCOLS>