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: 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.
Alanine is one of the most common AA's in a real-life helix, yet we are still penalized for incorporating it into our designs.
Many times an alanine in a helix would have fit better into a protein I'm designing than what I am allowed.
I am aware that many of the scripts we use here favor alanine-heavy structures, so that would somewhat limit the diversity the scientists crave. But instead of banning the sidechain, why not set a limit (5%?, 10%) on the number of alanines in helices before a penalty kicks in?
Yes, that is exactly what we would like to do (i.e. set a limit for the entire solution)! This got bumped down the to-do list by the latest AlphaFold features, but we still hope to implement it soon.
To implement it is slightly more complicated than you would think, because the Mutate algorithm assumes that all residue scores are pairwise-decomposable, and a "global" limit violates this assumption. However, we have a way around this now and hopefully we will soon be able to ditch the SS Design Objective.