The Partition Puzzles released yesterday were posted with the wrong score function, unfortunately. The old puzzles have been pulled and reposted with the correct score function. Players may load their work from the previous puzzles into the reposted puzzles. We're sorry for any inconvenience (but we're glad we caught the error early)!
Also, we'd like to apologize to LociOiling, whose tournament submission was misattributed to Newton76. This has been corrected in the blog post, and the reposted Partition Puzzle here. Sorry LociOiling and Newton76!
Looks like Exploration is not a score on these puzzles - you don't get more or less points based on meeting it. It's just a yes-no condition that redlines your current score if your protein backbone shape is not different enough from the original design. When the score is redlined, you don't get credit for it. As soon as you remove the red line (by getting RMSD above 2.5 A), you get credit for the score.
From Wikipedia: "In bioinformatics, the root-mean-square deviation of atomic positions (or simply root-mean-square deviation, RMSD) is the measure of the average distance between the atoms (usually the backbone atoms) of superimposed proteins."
In the Partition Puzzles, the Exploration Objective simply uses RMSD to measure the "dissimilarity" between a pair of structures: your current structure and the starting structure. The idea is that we are only interested in solutions that are dissimilar from the starting structure. So if a solution is too similar to the starting structure (i.e. RMSD < 2.5 Å), the solution is invalid and its score will not be registered with the leaderboards. If you've played any Foldit puzzle in the last five years that used the Exploration Condition, this is the same feature.
In the early days of Foldit, there was a completely different type of "Diversification" puzzle that used a different method to measure solution diversity. In those puzzles, diversity was measured between all player solutions (not just a pair of structures). That type of puzzle has been deprecated and is no longer in use. If you're a newer player and don't remember Diversification Puzzles, then don't worry about it—that method was more complicated than the RMSD metric, and I don't think it will help you understand the current Partition Puzzles. However, if you're curious about some Foldit history, the Diversification Puzzles are explained in this 2011 blog post.
I wonder if these puzzles would be easier
if they had a score bonus that depended
on the RMSD from the starting structure.
This score bonus could be as follows:
RMSD*400 points for RMSD<2.5 Angstroms
1000 points for RMSD>=2.5 Angstroms
This type of bonus would help Recipes
gradually convert structures with small RMSD
to ones with RMSD over 2.5 Angstroms.
You could keep the condition that to receive
credit, structures must have RMSD over
2.5 Angstroms.
You could also remove the RMSD bonus
from the scores when making the partition
functions for these puzzles.
Would it be easier if these puzzles had numbers?
The original Phase Two Partition Function Puzzles
could have numbers like 1575a-t, with the 20 letters
a-t being a shorthand for each designer's player
name. The revised versions (B right now) of these
puzzles could have numbers like 1576a-t. Also,
if an individual puzzle, like 1576d, needs to be
revised, it could be reposted with numbers like
1576d2 1576d3 etc.
Of course, if any puzzle gets revised and reposted,
it would be nice if a notice like 'Puzzle Expired'
would appear in the top-center Rank/Score box of
any Foldit client running an old version of the puzzle.
It would also be nice if we could upload our solutions
from previous versions of a puzzle into the latest
version of that puzzle.
It's a good thought, but chances are that those solutions which are going to be truly effective in "winning" these second round partition function challenges aren't likely to be the ones which just meet the 2.5 Angstrom cut-off. Remember, the goal here isn't simply to get the highest energy structure or the structure closest to the native. The goal in this second "challenge" round is to come up with structures which "break" the partition function/folding funnel of the design. (Or rather, to point out the existing flaws of the folding funnels of the designs.) Structures close to the design aren't unlikely to be quite as effective in "breaking" the partition function as ones which are further from the design structure, and the more structures you can come up with that differ significantly both from the input and from each other, the more you're able to "break" the partition function.
We can't say for certain, but chances are the people with the most success in these puzzles aren't going to be those who just make minor alterations to the input structure. Instead, I'm guessing that the people with the most success in this round will likely be those who pull the protein apart and then refold it into new and different structures/topologies.
That's sort of the reason for including the RMSD filter in the first place. We don't want you spending a lot of time/effort in structures which are more-or-less the same as the design. These aren't going to be successful in achieving the goal of this second round.
Perhaps an RMSD-dependent bonus would
help more than it hurts. The 3 conformations
for fiendish_ghoul's design shown at: https://fold.it/portal/node/2005620 and https://fold.it/portal/node/2005623
differ mainly in where the 3 helices are
placed with respect to the sheet made of
3 parallel b-strands. This reminds me of the conformational isomers of butane:
which can interconvert by rotation about
a single bond. In butane, 2 methyl groups
are moving around a covalent bond. In
fiendish_ghoul's design, 3 helices are
moving around a 3-stranded sheet.
Perhaps the RMSD-dependent bonus would
be enough to help a protein convert from
one conformation to another, while keeping
much of the structure intact. If nothing
else, an RMSD-dependent bonus would
give another, more automated, avenue
for exploring the conformations and
energy landscape of each given protein.
