What strikes me is that a simple mutate and wiggle round (with frozen interconnects) will up the score so much that I wonder if this is an early stage version of Steven Pletsch's solution or an intentionally downgraded version. Is there a story behind this ?
this was one i made quickly and abandoned in favor of another design, i simply didn't like a big 3 helix design because i thought it would be difficult to get a max core bonus
Thank you Steven. Still the mystery remains, when I keep the sidechains that make up the connections the score is lower than when I let these sidechains run free while mutating.
@bkoep; Should we keep the sidechains which are given, focus on the backbone to improve the score or let the sidechains mutate as well in order to optimize the score, possibly losing the current links (and optionally creating other links) with the spike protein ?
This design already has a nice-looking interface, so it may be sufficient to fix the loops and retain the given sidechains at the interface.
That said, there is always room for improvement! If we were certain about the given sidechains, we would have frozen them. Even though our binder metrics are not available to players yet (we're working on it!), optimizing your score is still a good strategy for finding an effective binder.
Has anyone thought that:
• The protein we are designing will fold as intended.
• That it will bind to the virus active sight as intended.
• That the virus, sensing it’s a cell wall, will destroy it.
Just an idle thought.
>>>>> Aubade00/01
try to make it better but nahhh
Residue Count (max +440)
Penalizes extra residues inserted beyond the starting 196, at a cost of 55 points per residue. Players may use up to 204 residues in total.
Interaction Energy (max +500)
Monitors that all PHE, TYR, and TRP residues are scoring well.
Core Existence (max +2400)
Ensures that at least 28 percent of residues are buried in the core of the monomer unit.
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.
SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.