Quest to Native results!

The results from the recent Quest to the Native puzzles have been very interesting. In these challenges we gave you a starting structure generated by rosetta@home that was far from the native structure, but included a ghost of the native protein to guide your folding.

The figure below shows the final results for "Quest to the Native 1".
On the y-axis is the Foldit score and on the x-axis distance from the native structure (closer to the left is better). The green dots represent the over 13,000 predictions that Foldit players have generated. The red dot at the bottom right is the starting Foldit puzzle,

There are two notable things about these results. First, it is clear that you have collectively mastered the tools implemented in fold.it so that you can generate a very accurate model starting with a quite inaccurate one. Second, there is an important lesson in the distributions of scores in the figure. Starting from the puzzle (the red dot), many players were able to increase the score without making very large changes in the structure (the score increases, but the distance from the native structure stays roughly the same). A second group of players made much larger changes in the structure, and were able to achieve much higher scores in doing so.

Of course, in real life puzzles the structure won’t be known already, so there won’t be a guide. But the two points above still hold. First, it is almost certain that you can get to the correct structure from the puzzle starting points with the tools in fold.it—but of course you have try out a number of possibilities because there is no guide. Second, while you can likely improve your score by searching close by the starting point, this is probably not where the real jackpot is—to get very high scores and to reach the native structure is likely to require more substantial changes in structure, similar to those in the Quest to the Native puzzles.

So the most important take home message is explore as much as possible, and don’t be afraid to stray from the starting puzzle conformation. In all hands competitions, consider the various possible starting points, not just the highest scoring, and again don’t spend most of your time really close to the starting point.
Like in science and many other aspects of life, innovation is the key to success!

I want to thank all of you again for playing fold.it—you are I believe showing the way to a completely new and powerful approach to key biomedical research problems and scientific problems more generally. We will soon be writing a paper describing your collective efforts that will announce this new approach to the scientific community.

( Posted by  David Baker 69 1797  |  Mon, 06/01/2009 - 17:54  |  5 comments )
8
Joined: 11/20/2008
Groups: None
:)

Thanks for showing those results, very interesting.

Joined: 12/14/2008
indeed

Very intersting. 2 points I would conclude:

1. From the screen it seems there were 6 major breakthroughs needed to the goal.
That would most likely be rebuilds of specific areas.

From that you could conclude that early rebuilding has a far greater chance of getting to the best score, while later on it tends to get stuck in local minima.

2. The approach of the players in this puzzle was different from normal.
In other puzzles you have only the overall score to measure. So you work on the score.
In this one you had the backbone shape. Players didn't bther with the score, but tried to rebuild the backbone and then improve the score.

= There should be improvements in both playing and tools.
1. Players: to put it short: be more flexible. (hard to do! It's not normal human pattern to use the unknown sideways if you can take the big roads to a before unvisited loacation.)

2. tools: Other measurements. Like a regional score: a score of all part between two frozen parts (or something like this).
[I shold have written somewhere about a local score comparism tool using what is displayed now with "ctr+i" that is concentrating on an even smaller area]

Joined: 06/12/2008
Groups: None
I agree

I must agree with LennStar. Region score could be very helpful. I think we need also some new tools for sidechains manipulating.

Joined: 07/07/2008
interesting

Is there any way to see graphs of this sort, but simply basing it on difference in structure from given structure, and total points?

infjamc's picture
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Joined: 02/20/2009
Groups: Contenders
Just out of curiosity...

Would it be possible for players to look up their RMSD (distance from native) for their highest-scoring solutions in the Quest to the Native puzzles?

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons