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Fold.it..."fold it good"

Tara DuncanAug 31, 2016, 3:59:57 PM


[Originally published on Facebook, May 2, 2016 - I'm almost ready to try this game again :)]


As I write this a folded protein is slowly revolving, and gracefully undulating on my computer screen, while the computer program runs a constant series of simulations on how to complete and optimize the fold. Not really, that statement was utter crap. The protein depiction is just sitting there impotently in the fold.it program, as I try seemingly endless combinations of backbone manipulating, structure changing, side chain wiggling, moving and shaking, to transform this graphic representation into the folded protein of my dreams. In case the initial reference is too vague, I should mention, equally vaguely, that I'm a huge Douglas Adams fan.


I was first introduced to the protein folding "game" over five years ago. I never worked up the enthusiasm to try it until recently. It turns out that gamers, mathematicians and science majors are more adept at creating viable, functional proteins, than the computer programs designed for this task. While it is certainly possible the computer construct could ultimately produce an equal or superior product, humans are apparently just better and faster at making this happen. Why is this an important activity? Well, we're constructed from various combinations of proteins, originally amino acid chains which your system cranks out and assembles into interesting shapes and configurations - much like linked sausages. Finding out why something works, why it fails initially or during replication, and discovering how to combine amino acids to create vaccines or protein "patches", for instance, is instrumental for medical science. This "game" is contributing to building better, more effective vaccines, and understanding and curing conditions and diseases.


The creators of this game clearly have gamers pegged. There is a lovely screen display, various sounds associated with various activities (I'm not a fan), a point-scoring system in real time, a leader board showing your relative rank, and the ever-motivating RANK UP! or RANK DOWN! Rank Up! Master Sergeant Protein Folder! I guess you have to love computer games to get the narcotic lure of this one.


This is not a fast activity, especially when you're working with large protein folds. There are some aspects of the experience I don't enjoy, such as the constant entreaties for politically correct speech in the message section. I'm not done with the game yet, so I just quietly fume when I see messages telling some hapless communicator that using ****ing in the chat is inappropriate. This did not refer to an actual word, just four asterisks ending with an "ing". I took the time to investigate how many word combinations were possible with four letters and "ing". There are literally hundreds, and I'm not a fan of pre-crime. Oh well...not my site.


Anyway, my current issue is this. I have recently completed the intro puzzles, the ones that familiarize you with the interface, methodology and goals. When moving on to the open protein challenges, I had some moments of clarity which allowed me to vault to the top positions with several of the puzzles. I should mention here that the leader board displays both your best score, and your current score. So while you're working on any given puzzle, you can see the numerical scores of other players (incrementing or decrementing in real time) as they work on their folds. In some cases you can see the people whose scores you have surpassed, methodically folding, wiggling, shaking, recombining, etc. their proteins, for hours and even days. Some of these people seem to take being bested very personally, and will work on reclaiming the top spots, to the point of obsession. I guess I'm there now.


For a while I had an award winning puzzle, based on nothing more than its top score. Over the next week, one, then two, then four people blew by me. The current top puzzle has about 200 more "points" than my best build which is rated at 8483 points. There may be others vying for the top 5 spots. You can usually see several people working on their puzzles, gaining several points at a sitting. It's sort of like watching a dog running toward you in Saskatchewan. It isn't fast. It isn't close; but if it keeps up its electrolytes and continues to run, it will eventually get there.


The fact that there are higher rated scores is not what really bothers me. My current issue is that, not only can this protein fold not apparently be improved, but any change I make, however small, demonstrably reduces its score. I have tried as much of "everything" as I can think of to date. I have tried building the whole thing from scratch, but the best I can do is to make it into the top ten. So, I apparently can't reproduce something I easily did earlier, and I can't make what I created any more impressive - only less so. It is reasonable to believe that some combination will produce a better result. We have only to look at the scoring mechanism to see that four people have done this. Oh well, I guess I'll poke at it some more.


If you're a gamer (or anyone who likes a puzzle challenge) you might want to give folding proteins a try. According to the scientific community (no peer review included so you can research if you're interested), the payoffs are already huge. If you have an addictive personality, however, be aware of the time/success ratio, and the possibility that some of the results (at least at this point), seem to make no logical sense - yet anyway. Whether you participate in curing a disease, exercise your brain, or simply have time to waste that should still result in some sort of productivity, protein folding is kind of awesome, in an awesomely frustrating way.


Fuck it. I've deleted the whole game.