Residue Count (max +550)
Penalizes extra residues inserted beyond the starting 205, at a cost of 55 points per residue. Players may use up to 215 residues in total.
Core Existence (max +2400)
Ensures that at least 28 percent of residues are buried in the core of the monomer unit.
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, SER, THR in helices.
What was the reason for removing the BUNS filter? I thought a minimum number of BUNS was necessary for good core formation and a stable structure.
BUNS are more of an issue when designing interfaces between binders, because polar atoms are required at the interface to solubilize the monomers, but these polars need to make HBonds in the bound state. In this case, all buried atoms can be nonpolar since we only want the linker to fold. We have no bound and unbound states.
MikeCassidyToday at 12:11 PM
Clicking on the Puzzle name in the App window is not opening up the puzzle in my www browser
Worked fine for me, Mike! Windows 10, Microsoft Edge
Hey Mike--is it working for you now?
Wiggle is acting very strange on this pose (Linux/main). The score initially increases but then decreases to a value below the original. Seems unrelated to filters or wiggle power. Scientist-shared the offending pose as "bad wiggle 34896"
This looks related to Building Blocks that have been inserted into the Blueprint panel.
The Building Blocks add torsional constraints that try to push the backbone toward ideal phi/psi torsions. This helps to promote backbone patterns that are common in known protein structures, but these constraints (like rubber bands) can cause loss of points during Wiggle.
tx bkoep: it's so easy to forget about those!
Yes, that's a problem that was never meant to persist. We had always planned to create a visual representation that shows Building Blocks on your solution, but it keeps getting pushed down the to-do list.