We are excited to let everyone know that the first Foldit "trophy" has been delivered! You may remember that Boots McGraw's design for the puzzle "187: More Core Design" (http://fold.it/portal/node/986677) was the first Foldit design to be tested in the lab (http://fold.it/portal/node/986908) - although the lab test didn't work out as we'd hoped (http://fold.it/portal/node/987148). To celebrate, the people at 3D Molecular Designs (http://www.3dmoleculardesigns.com/) were nice enough to make a model of Boots' design and donate it to us!
Here are some photos:
He says, "I will bring it to the office and leave it on my desk; so when my co-workers once again ask why I don't want to play 'Farmville' with them, I will show them the model and tell them I am 'busy curing cancer, AIDS, and the common cold'".
Thanks Boots and thanks to everyone for their contributions to Foldit! We'll continue looking for ways to reward our players!( Posted by Seth Cooper 87 1969 | Mon, 04/05/2010 - 22:23 | 6 comments )
Mini-CASP 17 Voting Results!
The solved structure for Mini-CASP 17 was just released and we have compared the native solution to your votes from the first 'Solution Voting Puzzle'.
Using GDT (Global Distance Test), which is the metric used by the assessors in CASP (the higher the number the closer to the native), you can see that 26% of you selected the Foldit prediction which was the closest to the native:
33% of you selected 'Solution 2' which had a GDT of 44.4
26% of you selected 'Solution 5' which had a GDT of 67.0
18% of you selected 'Solution 3' which had a GDT of 65.1
18% of you selected 'Solution 4' which had a GDT of 65.7
5% of you selected 'Solution 1' which had a GDT of 61.6
We are reposting '272: Mini-CASP 17 - More Alignments' as a Quest to the Native so that you can see the native and see what alignment changes needed to be done in order to get closer to the native state. For example, you'll notice that the template that started with the highest score (top alignment with a score of 127) does not get you closest to the native after a simple threading.
You'll also notice that this Quest to the Native is missing the first 9 residues, the starting extended chain has been trimmed as well as the query sequence in the alignment tool and the native guide. This is because the solved native structure does not have those 9 residues fully defined, the N-terminus is disordered. You can see this in the above video clip of the native structure.
Sometimes the functional parts of proteins are disordered until they meet their native partner, such as zinc fingers (which need the zinc to fold).
This will happen during CASP; they might give us a long sequence to work on, but once the structure has been solved they will only be able to assess a subset of that sequence in our predictions.
We will try to do our best during CASP to trim regions that are obviously disordered, until then we hope this Quest to the Native will help you improve your alignment tool skills for CASP 9!
If you want to examine this native structure in more detail:
Hold It! Results
Thanks for surviving my various biotin puzzles! I know some of the restrictions have made them very difficult. We've been experimenting with various puzzle setups and I think we'll soon find a happy intermediate between impossible and hard. :)
As for the results of the previous puzzles, I was pleasantly surprised with some of the solutions that were turned in. I'm curious to know whether any of you were able to find any strategies that seemed to work better than randomly searching. In future puzzles, I will include those solutions along with some others we have generated as the starting structures, with the primary goal being to maintain the hydrogen bonds while also pursuing the best packing score. We have a few more tweaks to apply, but be confident that I won't ask you all to do the impossible anymore. (find those bonds from scratch).( Posted by austinday 87 1969 | Sat, 03/20/2010 - 21:07 | 0 comments )
New Solution Voting Puzzles
CASP 9 is going to start on May 3rd, and we are very excited that this year Foldit will be its own CASP structure prediction group. Unlike CASP 8 where Foldit submissions were part of the Baker Team, this summer all of you will be part of 'The Foldit Team' competing against structure prediction labs from around the world.
As you might already know, CASP lets you submit 5 models for each target, so we have been trying to think of cool ways to let YOU, the Foldit players, pick these models (other than the top scoring Foldit solution which we plan to submit as one of the 5 submissions).
Today we are trying a new puzzle type where you get to vote for what you believe is the best model. In these "Solution Voting" puzzles, you will be given different high-scoring Foldit solutions from a previous puzzle. In today's case you have 5 Foldit submissions from puzzle 266: Mini-CASP 17.
You can look at each solution in gallery mode, rotating them around and comparing one solution to another using the guide, and then vote for the model you believe is better. You can show clashes, voids, exposed residues, bonds, and sidechains, but there is no score information given so you can't just vote for the one with the best Foldit score. All of these models are already very good-scoring Foldit solutions, and we're interested to see if you can pick out good models based on your own ideas of what proteins should look like.
Once the native structures are released, we will let you know which model was the closest to the native and will assign you points based on how close your vote was to the native. We haven't worked out all the details for that part yet, but the more "Solution Voting" puzzles you participate in and the more often you
vote correctly, the higher your Foldit rating will be. The skills necessary to rank good models might be a Foldit skill that we haven't measured before. As such, we might have to come up with a new ranking category:
We will test this out before CASP 9 begins, and if it seems to work well, Foldit might be able to participate in one of the other CASP categories: Quality assessment of models (http://www.predictioncenter.org/casp9/index.cgi#scope), where the CASP organizers give us a bunch of predictions and we have to rank them (which do we think is closest to the native). This could also be a very exciting category for Foldit players as well!
For now, please try out the new 266: Mini-CASP 17 - Solution Voting puzzle. We picked 5 different Foldit predictions from puzzle 266 for you to look at. For this first puzzle we expect to get the answer very soon, perhaps even this week. We don't know what the native looks like either, but since you've been working very hard on Mini-CASP 17 we hope you all might be able to make an educated guess!( Posted by beta_helix 87 1969 | Wed, 03/17/2010 - 05:54 | 0 comments )