Introducing: Foldit Lab Reports!

We're excited to introduce Foldit Lab Reports, a monthly video series with bkoep and others on the Foldit team!

The purpose of this series is to share more with Foldit players about what happens behind the scenes of Foldit. The videos are meant to provide brief, informal summaries of recent activity in Foldit and in the lab. Although they may not be as informative and detailed as some of our blog posts, we hope they will stimulate more discussion, and we encourage players to ask questions and leave comments on the website!

Check out Foldit Lab Report #1 on YouTube now!

NEWS
- The Foldit team is growing!

PUZZLE UPDATES
- Symmetric protein design with smaller interfaces
- Final rounds for IL-7R binder design

LAB UPDATES
- Promising lab results for symmetric homo-dimers
- Baker Lab scientists adapt Foldit designs for hetero-dimer project

BONUS UPDATE
- The Aflatoxin Challenge returns

(Tue, 10/01/2019 - 16:00  |  17 comments)
NinjaGreg's picture
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Awesome!! Love to see some of the faces behind the project!

Also, it seems to be a much more high-throughput means of information transmission than the chats, which I like.

A question about limiting the hydrophobes in the interface: doesn't that lead to more "open" designs, that is design with holes in them? Would those be as stable as the more compact designs?

Also, the sheer number of iterations of the IL-7R puzzle probably had a declining number of unique designs rapidly, since the scoring functions put a premium on conformity more than originality. I know I quickly learned that helix-based designs scored best, so tended not to do ones with sheets.

Thanks for doing the video!!

NinjaGreg

bkoep's picture
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Good question!

With the limited interfaces, you are right to be wary of designs with holes (voids) at the interface. These are very unfavorable for folding, and should be avoided. We're hoping that players can orient their monomer units to share a moderate-sized interface, without introducing holes (e.g. maybe helical bundles that are slightly offset from one another). This can sometimes be tricky to get right—especially in higher symmetries like the C3 trimers.

Yes, IL-7R puzzles are very constrained and players don't have as much to work with, so we don't expect a ton of diversity in folds. However, even similar-looking helical bundles can have very different amino acid sequences, so I think we will still see plenty of diversity at the sequence level. I would still encourage you to try out different strategies in each puzzle, if you can! Helical bundles do tend to score well, but we don't know which folds will work best in the binding experiment!

phi16's picture
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Congrats. Great way to share information, comments, etc.

Congrats, BKOEP. This is great. I often miss chats with scientists and miss being able to ask questions. This is much better than written blog posts. It's also great to put a face to the Username. Part of what makes FOLDIT great is the interactions encouraged between players and players, and players with devs. and scientists. Sharing via teams, the chat window and message boards are what FOLDIT is all about.

As a non-scientist, I often wonder whether my thinking about proteins and protein behaviors have any connection to reality. It would be nice to be able to ask questions and discuss proteins in general here. Thanks for all your work. phi16

Joined: 05/19/2017
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Ooh, videos!

I've been always on YouTube for a while so this is great! Also way easier to digest than the typical blog post, but there's a good time and place for those. I'm really happy to hear Aflatoxin's coming back too. Keep them coming!

(As an aside, if anyone's wondering where I've been; pharmacy school and being involved there has sapped my time and energy to livestream Foldit over on Twitch lately. That being said, I just got back from TwitchCon, and after meeting with fellow streamers from The Knowledge Fellowship, I'm trying to muster the energy to stream again, so look out for that. Twitch as a platform is also useful for live Q&A or podcasting, so if a longer form discussion video is in the cards, contact me!)

Susume's picture
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Great to hear

Great to hear what's going on in the lab!

What protein is the 3D model on your desk?

bkoep's picture
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That's Foldit1!

I also have 3D-printed models for Foldit3 Peak6 and Ferredog-Diesel. They are helpful for demonstrating the power of Foldit players, when we have visitors at the IPD!

Susume's picture
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Ha!

I saw that pi stack on the helices and had an intuition!

NinjaGreg's picture
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Another thought

I think we all feel a sense of pride/ownership of the proteins we fold, so it would be gratifying to hear when one of our design gets used by other scientists, even if it doesn't result in anything. I would help us feel like we're contributing to progress. For evolved designs, letting the group know would be great. Don't know how hard that would be to do, but it's a suggestion.

bkoep's picture
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Good to know!

That makes a lot of sense, and we've been thinking about ways we can communicate this better. Right now we don't have a good way to track and share this information easily, but we have a few ideas in the works that may improve things in the future!

Joined: 09/24/2012
Groups: Go Science
"I'm bkoep"

Excellent !

This is professional and fun. Exactly what we like in Foldit.

Welcome to neilpg628 ! (next time he'll have to say "Hello, I'm neilpg628")

Joined: 09/24/2012
Groups: Go Science
A suggestion

Not sure I understood well, but what about a follow up (second round) puzzle with old monomers (a selection of 5 player's top ones + the possibility to take one of our former solutions) ?

bkoep's picture
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Clarification?

Are you thinking of the symmetric design puzzles? Or the IL-7R puzzles? What would you like to see follow-ups for?

bkoep's picture
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IL-7R Update

This video is already obsolete! We got some additional sets of binding helices from bcov, so the IL-7R series will extend to Round 22.

This means more opportunities for Foldit players to design binders for IL-7R!

spvincent's picture
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Thanks for doing this bkoep:

Thanks for doing this bkoep: I think this is a great way to communicate. Look forward to seeing future videos.

jeff101's picture
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Very exciting

I really liked this video. Thanks for posting it.
I also liked seeing your white board at 2:54.

alcor29's picture
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Terrific.

Thanks for doing this. Hope you can keep this up. Blog posts still may be necessary when we need written technical info that we may need to refer to.

frood66's picture
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this is sensible

I'm real pleased to see this.

The content is good - and it is community orientated.

Nice one bkoep!

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