The Date: 17 February 2015 (Tuesday) Add your questions to this post!</a>
The location: #veteran, IRC (Get help with chat here.)
The Time: 1500-1600 (or so, but the official chat ends after an hour) PST
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The Topics: Science chat, with a likely Foldit drug design update as well.
The rest will be determined by you! (Please keep in mind we do read all your feedback posts, so no need to duplicate your posts that exist there.)
Looking for inspiration? Follow-up on previous topics? Read our previous chats.
We can't wait to see you there.
In some Design puzzles, we see information that "The Baker Lab will run folding predictions on your solutions for said puzzle, and those that perform well will be synthesized in the lab."
I've looked on the Blog and specific Puzzle pages and don't see that those results are made available to us. Do these results ever get posted and if so, where? It would be nice to see these results - even though I might not be able to understand them :)
Thank you.
We have posted some of these results sporadically on the blog, though nothing recently (see here, here, and here).
I agree that it would be great for Foldit players to get more feedback from the scientists. We can try to be better about this in the future!
In fact, we just ordered another batch of genes for some Foldit player designs, so I'll put together a blog post later this week!
Thank you and keep up the great work.
In addition, would it be possible to see picture (or documentary video) of your real lab, where we see the "visible" operations (if possible with some idea on the time needed for each step).
I would simply be curious to see what happens in practice: is this synthesis in small tubes, in big machines and so on.
What do you do practically as chemistry? like starting with an H2O solution, adding x grams of this and this product, this and this amino acid, heating, cooling, mixing or whatever, evaporating, …
It can be very pedagogic, very general for a large "child" audience, no need of the exact formulas (but you can link to available documents of course).
To see a mixture of proteins in solution. Then also a "electron density" machine (is it a huge machine? a small unit? an electronic microscope with some computer extend?).
Very basic but in order to "visualize" what you mean by "synthesizing in the lab".
Only pictures with legends are good as starting point.
1) What you try to do, is it almost "exactly" what our body does (in 2-3 weeks ?) when trying to construct an antibody against an antigen?
2) Is there an idea how our immunatory system "recognizes" a potential target on an antigen? How does our body know what to synthesize? (we folders "see" a hole and we try to stiff something in it, but our body?)
3) Are there examples of successes in medicines synthesized by the way you investigate? (folding target, folding potential medicines in function of this, synthesizing, then of course in vivo tests)? or is it still fundamental research?
Thanks for the Science chats !
In CASP 11, the Baker lab did much better on the contact targets than the foldit teams. Is there still a place for foldit in contact-based prediction? What changes are you thinking of for contact puzzles in the future?
There have been top solutions for abeta, is there a need for further refinement of those results (even if no points would be given) ? Are there other science puzzles that would benefit from further refinement ? For example with sidechain optimizations.
New hardware has arrived here and new approaches have been developed from which this process could benefit.
How about releasing open science questions as 'all hands' puzzles starting from previous top solutions ? (ebola, abeta and the like).
Basically, can you post or send out graphs after each puzzle ends showing the Foldit score on the vertical axis and the alpha-carbon rmsd (or some other measure of similarity with the best-scoring structure) on the horizontal axis?
Having custom graphs for each Group and/or Player would be great too. You could color the Group or Player's solutions differently from all the other Foldit solutions generated for that puzzle. This would help us see how close we got to the best-scoring structure. It would help us see and learn to control the diversity of solutions we generate. It would let us study questions like "which Recipe gives more diversity, DRW or GAB?"
The Feedback below gives more details:
http://fold.it/portal/node/988112#comment-28798
Thanks!
Jeff
