Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -200 points per atom (not including symmetric copies).
Core Existence: Monomer (max +2000)
Ensures that at least 20 residues are buried in the core of the monomer unit.
Core: Complex (max +0)
Awards no bonuses or penalties. Click Show to see which residues count as "Core" for the H-bond Network objective.
H-bond Network (max +2400)
Rewards networks that comprise at least 2 H-bonds involving core residues.
Between 1 and 12 H-bonds should cross the interface between symmetric units.
Networks must be at least 75% satisfied (i.e. 75% of all bondable atoms in a network must make a H-bond).
Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.
SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA 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 would be helpful if web pages like this for future
Symmetric Design Puzzles would say how many residues
are in each monomer.
Next, it would be nice if some tetramer puzzles would
flip adjacent monomers with respect to each other. I
think most of the tetramer puzzles so far have had all
4 monomers pointing the same direction (you might call
this a uuuu (all-up) configuration), but some tetramer
designs I'd like to try would work better with a udud
(up-down-up-down) configuration, in which adjacent
monomers point in opposite directions. It might also
be interesting to try designing tetramers with a uudd
Finally, I still have some trimer design ideas, so I
ask that you post at least one more trimer design