Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -150 points per atom (not including symmetric copies).
Core Existence: Monomer (max +1600)
Ensures that at least 16 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 +1800)
Rewards networks that comprise at least 2 H-bonds involving core residues.
Between 1 and 9 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.
If the idea behind the "Secondary Structure" objective is to discourage 3-helix designs, the 10-point-per-residue penalty seems a bit light...
Agreed. In a 90-residue puzzle, which typically can score over 20,000 points, having a 3-helix would only penalize the score 450 points, or about 2%.
You guys penalize 55 points per extra residue, 50 points for alanine in helices (when is this going to change?), and hundreds of points for a badly placed aromatic. Why not increase the penalty for too many helices accordingly? Fifty points per helix residue over 50% sounds reasonable. It deters, but doesn't prevent players from using the 3-helix bundle conformation.
Looking at previous puzzle results, we actually don't see much of a score discrepancy between helical bundles and helix/sheet folds.
Helical bundles are certainly more popular. But it is not uncommon to find a couple of helix/sheet folds in the top #3 solutions to a puzzle.
My guess is that helical bundles just take less work to design in Foldit (this is certainly the case in for other non-Foldit design methods). But, at the end of the day, a well-folded helix/sheet fold is a fair match for a helical bundle on the scoreboards.
The small bonus in this puzzle is just a nudge, but still it should be more than enough to outpace helical bundles in the top-scoring structures.