In Foldit, the basic score is calculated using an algorithm based on the Rosetta software suite. Some puzzles include additional "filters" that add a bonus or subtract a penalty depending on various factors. Particularly in design puzzles, filters help direct solutions toward specific goals set by the Foldit research team.
As of January 2017, the most common filters in design puzzles are:
- Residue IE Score
- Core Existence
- Secondary Structure
- SS Design
- Residue Count
- Ideal Loops
- HBond Network
Some non-design puzzles include a filter that rewards the formation of disulfide bridges:
- Disulfide Count
Contact map puzzles include a filter which award bonuses for matching predicted contacts.
Older Foldit design puzzles had "Layer Score" or "Layer Design" filters which evaluated several aspects of a protein's design. These filters have not been used in more recent puzzles, in part for performance reasons.
The typical behaviors of these filters are described in more detail below. The filters may vary in operation from puzzle to puzzle.
Design Puzzle FiltersEdit
Some or all of these filters may be found in design puzzles.
Residue IE ScoreEdit
The Residue IE (interaction energy) Score filter, found in design puzzles, typically monitors that the aromatic ring residues are scoring well. The aromatics are phenylalanine (PHE), tyrosine (TYR), and tryptophan (TRP). The filter applies a penalty if the interaction energy is too low.The segments with penalties are highlighted with red halos if the "Show" option for the filter is checked. When there's a penalty, the segment's "Segment Information" window shows the current interaction energy and the required value. In this instance, smaller the score, the better, so a negative IE score is better than a positive score. (Normally, Foldit presents scores as positive values.)
The Core Existence filter, found in design puzzles, rewards a hydrophobic core.
In symmetry puzzles, there may be two core existence filters: "Core Existence: Monomer" and "Core Existence: Complex". The monomer filter would be filter on a non-symmetry design puzzle (these puzzles usually have "monomer" in their titles). In a symmetry puzzle, the "Complex" core existence filter rewards the "interface" between the monomer units.
The Core Exists filter was described in a 2013 blog post. In the earliest versions, the filter was called "Core Exists", and in symmetry puzzles, applied to both the monomer unit and the interface between monomers. Later symmetry puzzles have two separate "Core Existence" filters for the monomer and the interface.
This follow-up to the 2013 blog post describes some considerations for refining the core of a monomer.
The Secondary Structure filter in a design puzzle places limits on how many residues are in a particular type secondary structure. Since helixes score well in Foldit, the Secondary Structure filter often requires that no more then 50% of residues are in a helix. This avoids designs which are mostly helixes. In several "More Sheets!" puzzles, the secondary structure filter was reversed, to require that at least 50% of residues are in sheets.
Secondary Structure DesignEdit
In design puzzles, the Secondary Structure Design filter limits which secondary structures can contain specific amino acids. This filter often disallows cysteine (CYS) entirely, while disallowing glycine, proline, and alanine in sheets and helixes.
Some Foldit design puzzles allow players to insert additional residues (segments). The Residue Count filter penalizes adds a penalty if the number of residues exceeds the stated maximum. For example, [Puzzle 1328] started with 85 residues, but allowed players to insert up to 10 additional residues.
The concept of ideal loops has been featured in recent Foldit design puzzles. The Ideal Loops filter penalizes loops between sheets or helixes if they depart too far from ideal constraints. Several new features, such as ABEGO coloring, the Rama map and the Blueprint tool are intended to help construct ideal loops. Also, puzzles with the Ideal Loops filter typically disallow use of the "rebuild" tool, in favor of the "remix" tool. A 2016 blog post contrasts remix and rebuild, and describes the new user interface features which make the remix tool easier to use manually.
Hydrogen Bond NetworkEdit
The Hydrogen Bond Network filter was described in a [2016 Foldit blog post]. The Hydrogen Bond Network filter awards hydrogen bonds that link a series of hydrophobic residues on the surface of a protein. The filter usually includes a requirement that network bonds across monomer units in a symmetry puzzle. [Puzzle 1103] included an assymetric version of the filter, which required the network to cross multiple non-identical chains in the protein.
The Disulfide Count filter is found on non-design puzzles. The filter rewards disulfide bridges. The filter is commonly used on "revisting" puzzles. When these puzzles were originally presented, there was no special reward for disulfide bridges.
The Contact Map filter is found on contact map puzzles, and awards bonuses for matching predicted contacts.
Layer Score / Layer DesignEdit
The related Layer Score and Layer Design filters were found in earlier Foldit design puzzles. They have been dropped in more recent puzzles.
Both filters significantly slowed down gameplay. In particular, some use of some long-running recipes became much less feasible. The ability to disable filters in a recipe led to recipes with "layers" or "for layers" in their titles. These recipes disabled filters during certain operations.
While the layers filters are gone, it's still common for Foldit recipes to offer an option to disable filters.