DsspDesign

Design residues with selected amino acids depending on the local secondary structure. The secondary structure at each residue is determined by DSSP (or read from a blueprint file).

All functionality here is included in the LayerDesign task operation, which is much more powerful. However, this filter has significantly reduced overhead by avoiding slow SASA calculations.

<DsspDesign name="(&string)" blueprint="(&string)">
    <SecStructType aa="(&string)" append(&string) exclude="(&string)"/>
</DsspDesign>

blueprint: a blueprint file which specifies the secondary structure at each position.

Below are the valid secondary structure types and the default set of allowed residue types.

Helix: ADEFIKLNQRSTVWY
Strand: DEFHIKLNQRSTVWY
Loop: ACDEFGHIKLMNPQRSTVWY
HelixStart: ADEFHIKLNPQRSTVWY
HelixCapping: DNST
Nterm: ACDEFGHIKLMNPQRSTVWY
Cterm: ACDEFGHIKLMNPQRSTVWY

The set of allowed residues for each secondary structure type can be customized.

aa: define the set of residues allowed for the defined secondary structure type; the string is composed of one letter amino acid codes.
append: append the following residues to the set of allowed residues for the defined secondary structure type.
exclude: opposite of append.

DsspDesign

DsspDesign

See Also