Hand Fold Proteins

[spmm]

so do you want to do that with every other repeated puzzle in foldit? there are a lot of them. Same logic applies.

[karstenw]

i think i need to reword the question. "karsten, if a protein was released 8 times in the same 4 month window and you were able to roll your solution over through all 8 proteins would you would ok with that right? after all, we do repeat proteins around here, so you then must follow the logic wherever it takes you. otherwise you are not consistent." You caught me…if we get 8 proteins and i manage to stay in the top r5 for all 8 proteins, i'll still cry foul from a gaming perspective. even though i'm not trying to stamp out repeating proteins entirely. ok this was fun, but i need to stop, i've exhausted all my arguments i think. thanks for the challenging conversation everyone. any last remarks will be read, but i won't respond anymore. i've cluttered the boards too much already.

[wisky]

Lots of good suggestions in here. I would really be interested in being able to actually see the native structures for a lot of these puzzles after the fact, and compare my individual fold with the native. I'm in the process of doing my first decent looking hand fold puzzle, thanks in large part to advice marie_s has given. At the end of this set for denovo 27, I would like to be able to compare my structure to the native structure (loaded as a guide) of the protein, and see where I could use improvements on my folding process/structure prediction capabilities.

Since the new wiggle came out, fuzes don't appear to working nearly as well, and they take longer. I've had to cut down considerably on the amount of fuzing I do in hand folding and non-hand folding puzzles because of this, and have started trying out new methods. My structures have also been consistently less chaotic looking, and more compact since new wiggle came out…

One possible way to account for the issue of structures not coming close to the native is a separate score/rank based on how close your structure is to the native, or even a score term that takes this into account. I realize a lot of these proteins might not have their native structures solved yet, but quite a few of them do, and some of the natives are released after a puzzle closes. I still think that should be able to weight the scoring better. Even with hand folding, you will still get a lot of false positives. Recipe only work (powerful recipes run on powerful computers) can produce high scoring false positive solutions. I know this, I've made first place on at least one puzzle (707 - http://foldit.wikia.com/wiki/Puzzle_707 ) with a false positive solution. gitwut's solution was actually considerably closer to the native fold than mine.

I know that my comment isn't necessarily about hand folding, but without a way to compare our structure to native structures, many players will have absolutely no way of knowing what better solutions look like (seeing a picture of it is NOT the same as being able to play around with it in-game) or how to create them.

@karstenw: You don't have to stop posting on this, I feel your comments have been very helpful in opening a discussion about the current state of hand folding.