Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -200 points per atom (not including symmetric copies).
Core Existence: Monomer (max +2200)
Ensures that at least 22 residues are buried in the core of the monomer unit.
Core Limit: Complex (max +500)
Checks that no more than 116 residues are buried in the symmetric 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.
It's easy to get independent monomers with 0 Buns. The bonus system doesnt encourage a polymer complex.
I can compensate the (probably too many) orange residues at the interfaces by having more green residues inside the monomer's core (instead of orange ones), which gives me full bonus.
Is this intended?
If there is no bonus for making H-bonds, then how do we know we have the monomers correctly making a complex? Is there some other metric that indicates we have what the scientists want?
I ask this, because all arrangements of the monomers that are close to each other that I have tried result in drastic score reductions, even when BUNS and clashes are removed. What's the point of bringing monomers together, if doing so doesn't result in improvement?