Thu, 03/31/2016 - 23:48
#2
Temporary residues?
The filter is intended to give players the flexibility to temporarily add residues to a design-in-progress.
How would temporarily adding residues be beneficial? Just curious.
Fri, 04/01/2016 - 01:13
#3
temp residue
make what was a sheet into a helix, switch another helix to sheet. can add to one, subtract from other without redoing whole fold. good for those of us with poor layout skills :D
Sun, 04/03/2016 - 22:20
#4
Performance Rama
Compared performance on several recipes.
The performance penalty varies between 10 and 20 percent.
I can not find real difference between the different tools wiggle, shake, mutate and rebuild, it looks like all tools are somehow effected.
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.
Residue Count: Penalizes extra residues inserted beyond the 65 residue limit. Players may insert up to 10 extra residues.