Upcoming Science Chat on July 18th

Science Chat July 18th in Veteran IRC

Hey there, everyone! I’m excited to announce that the upcoming Science Chat will be next week on Tuesday, July 18th at 8:15pm GMT (1:15pm, Pacific Time Zone). If you have questions for our developers/scientists it would be helpful to post them right here so the team can review them in advance. If we aren’t able to answer all your questions in the given time, we will attempt to get a blog post up soon with answers. We are looking forward to chatting with you all!

Date: Tuesday, July 18th, 2017
Time: 8:15-9:15pm GMT; 1:15-2:15pm Pacific Time Zone
Location: #veteran, IRC

Time Converter: http://www.thetimezoneconverter.com/

(Thu, 07/13/2017 - 20:47  |  20 comments)
LociOiling's picture
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Joined: 12/27/2012
Groups: Beta Folders
Mystery molecule from puzzle 1387b

Puzzle 1387b had a very strange molecule at segment 30. I'm not even sure if it qualifies as ligand, since it's spliced into the backbone just like one of the 20 usual suspects.

Among the odd features of segment 30 was a "shy" hydrogen that seemed to have an unlikely position.

What does segment 30 represent?


Ligand from puzzle 1387b - "front" view


Ligand from puzzle 1387b - "front" view


Ligand from puzzle 1387b - "front" view

tokens's picture
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Update on 1387b

Regarding 1387b are there any updates on whether the designs foldit players made seem to fold as designed in the lab, and if so, do they seem to bind to the hemagglutinin?

tokens's picture
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Joined: 11/28/2011
Dysferlin Linker Domain (puzzle 1390 and others).

Is there any way to check whether the predictions made by foldit players are close to the native fold or not? If so, what are the results?

Also, how come the contact map on this puzzle seemed so "chaotic/random" and how come it differs quite a lot from the contact map predicted by raptorx (see http://raptorx.uchicago.edu/ContactMap/myjobs/83006813_233351/ ).

Joined: 05/19/2017
Groups: None
Camera/Drag Controls

Are there any plans to refine the camera and dragging controls? Normally in editor/sandbox games that work in 3D, having some sort of axis alignment to dragging tools or camera really helps. Spore has really great examples of multiple 'thing' editors that give the player lots of tools to precisely (but more importantly, without frustration in 3D space) move little bits of their creation as they see fit. In other sandbox editors, player perspective is controlled in a 1st person fashion, with WASD+mouse aiming.

I ask this because in my "Sock's Lab" streams (https://www.twitch.tv/s0ckrates) there's a good example of controls getting in the way. Every time I wanted to drag some rubber bands out into 3D space, it is such an inconvenience to spend 5 minutes dragging the camera, repositioning, dragging the camera again, only to find out my molecule blows up in my face when I hit W because I dragged the rubber band into the foreground/background/molecule somehow and it snapped-to. If I just had little axis arrows at the tip of the rubber band that I could simply drag and slide it along an axis, that would already make it so much easier and smoother to get my rubber band to where I need it to go without accidentally sabotaging my entire conformation.

Controls are an important part of any game, and can be the difference between people continuing to play or stopping altogether. I would even go so far as to say Foldit could be a really nifty VR game...

Joined: 09/24/2012
Groups: Go Science
Are we less needed for unpredicted proteins?

In a paper from 2011, players found the structure of an HIV protein. We don't seem to repeat this success. Are we less accurate with our recipes? or don't you need us anymore for such kind of work?

bertro's picture
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Groups: Beta Folders
Any development on the Programmer side?

Any development on the Programmer side?

bertro's picture
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Joined: 05/02/2011
Groups: Beta Folders
Are the Drug Design puzzles coming?

Are the Drug Design puzzles coming?

Joined: 03/05/2015
Groups: Gargleblasters
Ideal loops bank ... a long question "shortened" (I hope)

Listening to a TED Talk on neuroscience where the neuroscientist was saying that variability can really bother scientists. Surmising that the ideal loop database intent is to limit the set of loops, I was wondering if the intention of that set (and the filters) is meant to limit the variability by a) excluding a larger set of loops that could make Rossman or Koga +Koga folds, and b) limiting the sheet and helix segment totals; (and perhaps the other filters) are also meant to drive the data in the direction of the types of structures that fit the scientists' theories (I realize this may be an error in my thinking). SO here's my question: Wondering if the loop, helix, sheet, and filter limitations might actually be introducing a “bias”.... and if expanding the library and changing limitations of the structure might actually produce more meaningful data. (after an initial period of relative chaos from a database standpoint)

(Here's why I had this thought: Using the brain example, the neuroscientist was saying how there was much variability between people’s brains and how they worked, and that variability was driving the scientists crazy… until they realized that was, if I interpreted her talk correctly, exactly that variability that might hold the answers as to why recovery from things like strokes was so difficult - they had limited themselves by thinking that the “ideal” brain science would produce cut and dried results… which it doesn’t … and the strategies for dealing with learning or with recovery from brain damage have been limited by that older - and as they see it now incorrect- view.)

Susume's picture
User offline. Last seen 1 hour 46 min ago. Offline
Joined: 10/02/2011
Design update?

Do you have any preliminary results from design puzzles 1306 and beyond?

Joined: 09/24/2012
Groups: Go Science
Ideal sheets: straight or not straight ?

Ideal SS sheets are not straight.

However, working with initial straight sheets seem to give more points at the end.

And tweak too tends to straight the sheets.

Are ideal sheets straight or not ?

Joined: 09/24/2012
Groups: Go Science
Ideal sheet-sheet Loops of 3 residues and Blueprint

Why doesn't Blueprint propose us a loop of 3 residues for connecting sheet-sheet ?

Joined: 09/24/2012
Groups: Go Science
Are we better in revisiting puzzles?

The results (in points and shape) seem always different. Are we better now than before ?

Joined: 09/24/2012
Groups: Go Science
OOOPS sorry
Susume's picture
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Novel designs

Have there been any novel-shaped foldit designs (shapes not found in nature) that have performed well in Rosetta or in the lab?

Susume's picture
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Joined: 10/02/2011
Hand crafted vs high throughput

Baker lab has had some recent success in producing thousands of small protein designs computationally. Is there still a place for hand-crafted designs like foldit players produce?

spvincent's picture
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Groups: Contenders
If you were going to add an

If you were going to add an extra amino acid to the standard set of twenty,as now seems possible, what would it be?

smortier's picture
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Posting this questions for a player:

"can we understand why the ideal loop library is so limited that one can not do a true Rossmann 2 by 2 fold? It would need some "yellow" glycine direction loops from sheet to helix. I asked on the last big protein puzzle. I want to understand if such a fold is not "ideal" -- seems odd to me as it occurs often in nature. I won't be on science chat, but ran my poor little machine into the ground trying one with 6 AA sheets and one with 8 AA sheets. I'd really like feedback"

smortier's picture
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Thanks so much for chatting with us today!!!

Here is the log of today's chat:

http://fold.it/portal/node/2003948

Aotearoa's picture
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Joined: 06/08/2008
Groups: Go Science
We are not getting credit anymore by the UW

Can anyone explain why we are not worth the credit we all deserve for our hard work and time designing proteins anymore?

http://tinyurl.com/yd2ozb7k

http://www.genengnews.com/gen-news-highlights/gene-synthesis-upgrades-protein-design-massively/81254665

To be given a little bit of credit would be great, otherwise we will have to start charging the university of washington to design their drugs and supply the research they cant otherwise get. Seriously.

Respectfully, Aotearoa
Renton Innes
New Zealand.

smortier's picture
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This is a different project.

This article is referencing work done by a different researcher in the Baker Lab. Foldit players were not involved in this research.

We always do our best to credit Foldit players because we are very appreciative of the work that you guys do. That is why Foldit players are often credited as authors on research papers, or if not, have credit in acknowledgements or author's notes (some publications won't allow groups to be listed as authors, so we have to work around that). We very much value our partnership and always try to ensure that credit is given where credit is due.

As always, let me know if you've any other concerns.

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