Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.
Core Existence: Ensures that at least 30% of the residues are buried in the core of your design.
Secondary Structure: Checks that no more than 50% of residues are in helices; penalties are incurred if more than 50% of residues form helices.
Secondary Structure Design: Penalizes all CYS residues. Penalizes GLY, ALA, and PRO residues in helices and sheets.
I would and probably others would highly appreciate it if there was someone who would not mind modifying mutate no wiggle from brow to recognise the criteria for the secondary structure design.
It would save a lot of time having to go back and allow GLY, ALA and PRO in loops.
Porky (soon to be parky)