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TaskOperation to allow only conservative mutations at designable residues.

Published Description

The conservative mutations for each residue type are composed of the substitutions for each residue which score >= 0 in one of the BLOSUM matrices (which are used for the seminal protein sequence similarity programs, PsiBlast and Clustal). All BLOSUM matrices can be used for conservative design. The numbers of the word BLOSUM indicate the sequence similarity cutoffs used to derive the BLOSUM matrices, with higher numbers being a more conservative set of mutations. By default, the conservative mutations from the BLOSUM62 matrix are used to strike a balance between variability and conservation.

Paper: RosettaAntibodyDesign (RAbD): A general framework for computational antibody design


<ConservativeDesignOperation name="(string)" residue_selector="(string)" data_source=(string,"blosum62") include_native_aa=(bool,"true")/>

residue_selector - By default, ConservativeDesign works on all residues. It will be confined to a selection of residues if a selector is provided

data_source - Set the source of the data used to define what is conservative. Options are: chothia_76 and the Blosum matrices from 30 to 100; designated as blosum30, 62, etc. Default is blosum62. The higher the number, the more conservative the set of mutations (numbers are sequence identity cutoffs).

include_native_aa - Include native amino acid in the allowed_aas list

See Also