Core Existence: Monomer (max +2400)
Ensures that at least 24 residues are buried in the core of the monomer unit.
Core Existence: Complex (max +4200)
Ensures that at least 84 residues are buried in the core of the entire complex (including the interface between monomer units).
SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA, SER, THR in helices.
Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.
Secondary Structure (max +500)
No more than 50% of residues may form helices. Extra helices are penalized at 10 points per residue.
It is always a pity when you are not able to delete residues at one end and stick them to the other end of the protein :(
This is a long-standing complaint, and we hope to correct it soon!
For obscure reasons, it is slightly more complicated to implement this for symmetry puzzles (insertions and deletions are more straightforward in the monomer design puzzles). But there are ways around this, and it's on our to-do list!