ProteinCore

Restricts design of residues that are in the core (e.g. to prevent charges). To determine which residues are core, it counts spatial neighbors (distance between Cb). To avoid confusion in turns on the protein surface, neighbors in sequence are omitted, similar to the way used in Choi & Deane, Mol Biosyst(2011) 7(12):3327-3334 DOI: 10.1039/c1mb05223c

 <ProteinCore name=(&string) distance_threshold=(8.0 &real) bound=(0 &bool) jump=(1 &Size) neighbor_cutoff=(10 &Size) neighbor_count_cutoff=(6 &Size) />

Option list

distance_threshold: maximum distance for a residue to be considered a neighbor
bound: removes chain(s) after jump to avoid counting ligand residues as neighbors
jump: jump between chain of interest and ligand
neighbor_cutoff: number of sequential neighbors to be excluded from calculation
neighbor_count_cutoff: number of neighbors required for a core residue

ProteinCore

ProteinCore

See Also