CASP 9 Brainstorming: Chat with Foldit Devs
In order to optimize our collective performance at CASP puzzles, we'll arrange a set of chat sessions so that we hear and discuss first hand the modifications to Foldit that will make the most difference to how good our predictions can be. Given that our players are spread worldwide, we'd like to find the best times when most people who would like to participate in the chat. To vote for your time, please go to the following link and select a range of times that would work for you. We will announce the chat times by the end of the weekend.
Looking forward to hearing from you all,
Zoran
zoran 127 4110 |
Fri, 05/07/2010 - 23:14 |
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All Hands is back!
First off: We will be posting the first CASP 9 puzzle later today!
Since CASP lets us submit 5 models per target we need a way to select which of your Foldit solutions to submit. Hopefully All Hands will be a good way for you to select these.
To test this out we are giving you top scoring solutions from puzzle 286 that are sufficiently different from one another.
All Hands shares these top scoring solutions with everybody, periodically refreshing the list.
You can view all of them by clicking "Open/Share Solutions" in the All Hands panel (which is a movable panel!). The solutions in this list will be repopulated often as you improve them.
Make sure to try working on all of the solutions (and not just the top scoring one) as the lowest scoring one in the list might be the closest to the native!
If you cannot see a solution after loading it, trying pressing Q to center the protein.
( Posted by beta_helix 127 1431 |
Wed, 05/05/2010 - 23:57 |
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Experimental tests of anti-influenza designs
We have now analyzed your redesigns of the last anti-influenza puzzle
and found the solution by user Vakobo to be extremely promising! Vakobo reformed a
loop into a helix introducing new hydrophobic interactions with
hemagglutinin which weren't there in the original design. We'll experimentally
test Vakobo's solution in the lab over the next few weeks and hopefully it will turn
out to be a binder. We'll keep you posted! Thanks to Vakobo and all of the other
participants in this puzzle. We hope that you'll participate in the new puzzles that
we've posted. We're excited to test your ideas!
sarelf 127 6665 |
Thu, 04/22/2010 - 00:44 |
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Suggestions for alignment puzzles
You are all doing great things on the alignment puzzles! Here are a few tips to keep in mind:
1) The biggest errors in the starting alignment will often be in strands at the edge of sheets. It is very hard for automatic methods to align these
properly. You may want to try shifting the alignments up and down several residues, allowing the loops before and after the beta strand to change in length
to allow for the sliding of the sequence through the strand.
2) Loop regions that are close to a sheet in a starting model may in fact be strands, so you might try converting the loop to a strand and making it pair in the sheet. A beautiful example of this is the miniCASP 14 puzzle. The highest scoring FoldIt solution converted a loop near a sheet to a strand, and totally nailed the correct solution. I found this extremely impressive!
3) Loop regions often vary quite a bit during evolution. Look carefully at the sequence alignment in the loop regions, and try shifting segments right and left where the alignment is poor. You will obviously need to spend quite a bit of time trying to optimize regions that are not aligned.
4) Regions where the sequence alignment is very good are likely to be correct, and it is probably wise to leave these more or less alone.
Congratulations on your work so far, and we are expecting great things during CASP which starts in less than a month!
Below is the top scoring Foldit solution (in green) for Mini-CASP 14 - Last Chance, the template that was used (in red), and the native structure which was released yesterday (in blue):
David Baker 127 2544 |
Thu, 04/08/2010 - 21:44 |
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Foldit trophy!
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 127 4110 |
Mon, 04/05/2010 - 22:23 |
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