Through the eyes of a scientist - Puzzle 1018

Embedded Video: 

Baker Lab scientist bkoep recently sat down with Foldit players' designs from Puzzle 1018 for a visual inspection, which is the first step in our analysis of Foldit designs. Join us as we take a critical look at the latest symmetric proteins designed by Foldit players and voice some thoughts about the really cool things Foldit players are demonstrating in protein design!

In the video, you'll also hear brief discussion on the following topics:

  • hydrogen bond networks
  • core packing
  • hydrophobic interfaces
  • special considerations when designing with GLY, CYS, and MET residues

We apologize for the inconsistent sound quality—subtitles can be accessed on YouTube with the "CC" button below the video frame.

Check it out and leave your questions in the comments below!

( Posted by  bkoep 78 1293  |  Tue, 12/16/2014 - 00:56  |  14 comments )
4
wisky's picture
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I love it!

Thank you very much for posting this :D I love it :)

Joined: 04/11/2013
Great

Thank you
Perhaps someone is smart enough to make a summary...things like having a small interface between each monomer...fewer hydrophobics between them and goods bonds...I think also you mentioned the monomer needing to be soluble and voids between monomers to be (avoided)...not sure about that last one.
Thanks again.

Joined: 08/10/2014
Can you upload a better video

Can you upload a better video quality version?

bkoep's picture
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Apologies

Sorry for the poor video (and audio) quality. We'll keep this in mind for future videos.

jeff101's picture
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Who made the structures you showed?

I bet the players and teams who worked on the structures you showed would like to see their names on the screen. While each structure is on the screen, you could list its Foldit score, its rank (solo or evo), the team name, the soloist, and any evolvers who worked on it.

spmm's picture
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brilliant thanks!

and a masterclass in Pymol thrown in :D
I would love to see more of these reviews, without you having to take the time to show score and names, but it would be good to get an idea of the relative score of the ones you thought were good but were not high scoring.
A big take out for me was the 'soluble monomer' concept and that maximising the 'contact' along the 'length' of the monomer is not necessarily essential.
thanks

Joined: 10/23/2014
Groups: Contenders
Thank you for the video

Your explanation definitely helped. My solution was more intricate than the top scoring solutions.

I agree with the comments of spmm. It would be nice to have another video commenting on some of the lower scoring solutions. You've given examples of mostly good designs. What would be helpful is to critique other designs in the 11-100 rankings. Otherwise I feel there will be an influx of similar looking designs in the future, which may or may not be what you want.

bkoep's picture
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Player information

In accordance with our Terms of Service, we do not associate analysis and player information without explicit consent from the player in question. It is unlikely we will include Foldit usernames or ranking statistics in such videos.

In addition, I'd like to stress that we do not look at player information when evaluating Foldit designs. This video is intended strictly to communicate scientific concerns in protein design; I would not want to give any false impressions about the use of player data.

bkoep's picture
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Thank you all for the feedback!

I am encouraged that so many players found this video helpful—perhaps we will do another one in the future.

Note that the only high-scoring structures addressed are the three designs between 16:00 and 22:00. All of the previous designs were "Shared with Scientists" and the final two exciting structures were buried deep in the stack of clustered solutions.

spvincent's picture
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This video was really

This video was really interesting and just the sort of thing I was hoping would be made : there was a lot of useful information in it, athough I'm slightly uneasy about the emphasis on helix bundles.

And I don't see any big issue in identifying players by name: it's not as if you're releasing personal information and player names appear in some of David Baker's videos.

Joined: 02/11/2012
Groups: Geekdo
thanks

Thanks for all the good work, and thanks fot taking such a deep interest in our designs!

Joined: 02/11/2012
Groups: Geekdo
PS

Add a phrase into your general rules of usage "player names may be freely released at any time" - I certainly don't mind.

jeff101's picture
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Below are recent talks by David Baker on similar things:

https://www.youtube.com/watch?v=4d7UxMvg5sU from Dec 2014
discusses symmetric solutions starting at 12:58.
5:41 talks about "Scientific Discoveries by Foldit players".
6:15 has a slide showing results from spvincent, grabhorn, and mimi.

https://www.youtube.com/watch?v=0LetJMbu7uY part 1 and
https://www.youtube.com/watch?v=ZrAwWx7meTk part 2
are more talks from Nov 2014.

Joined: 09/24/2012
Groups: Go Science
Very motivating ! Wants more scientific activity videos.

Interesting (even if I don't understand everything very well due to bad sound quality and my limited English knowledge).

We can all recognize similar designs we tried or didn't try. There is also the possibility to send pictures of our designs to the Wiki (so it's not necessary to disturb your scientific thinking by loosing time rewarding players):
http://foldit.wikia.com/wiki/Puzzle_1018b

I also like the non verbal reactions, like finding amazing the (I suppose) silverberg design. I had the same reaction seeing this design.

It's encouraging to see that uncommon designs can catch your interest. Good for our creative motivation. Why not inviting an artist to evaluate these designs with his/her artistic point of view? (I would not be surprised that some good proteins have also some nice harmony).

It would be interesting to see other such kind of video covering other parts of the scientific process, either:

-how a specific design is further worked and synthetized in the labo;
-how you further consider or evaluate "normal" revisit puzzles;
-same for other categories of puzzles (de novos ...)
-same, if possible, concerning strategies found in recipes
-same for the "game" and "social" aspect
-any post of conferences you made on Foldit, with anecdotes etc

Your feedback and "open doors" of your research activity is a good way to make us the feeling being a (small) part of your team.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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