New Paper!

scichat.pngFresh off the Nature press: Determining crystal structures through crowdsourcing and coursework. As the paper abstract notes, "Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure."

Good job, Foldit community! In celebration, we're also announcing our next Science Chat, and this paper of course, will be the main theme (but other science questions for Foldit are welcome). Be sure your questions get posted here.

The Date: 27 September 2016 (Tuesday)
The location: #veteran, IRC (Get help with chat here.)
The Time: 2100-2200 (or so, but the official chat ends after an hour) GMT (aka 1400-1500 PT)
The Time Zone Converter: Right this way!

(Fri, 09/16/2016 - 17:25  |  15 comments)
jeff101's picture
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The Nature paper:

The Nature paper's Supplementary Information is at:

http://www.nature.com/ncomms/2016/160916/ncomms12549/full/ncomms12549.html#supplementary-information

It contains extra figures, reviewer notes, and the movie below:

http://www.nature.com/ncomms/2016/160916/ncomms12549/extref/ncomms12549-s2.mov

jeff101's picture
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The Nature paper's movie:

Is there a timeline for what is going on in the Nature paper's movie?
It seems to be settling up until 1:25, and then it starts wiggling a lot.
Do certain parts of the movie show hand-folding while others show recipe-folding?
I wish it only showed moves that improved the Foldit score.

jeff101's picture
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The Nature paper's movie:

Would it be possible to post another version of this movie
that shows the Foldit score for each frame and only includes
frames that improve the Foldit score? Thanks!

brow42's picture
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Quicktime

FYI for future movies, Quicktime is obsolete, unsupported, and DHS advises everybody uninstall the codec: http://www.pcworld.com/article/3056625/windows/uninstall-now-apple-abandons-quicktime-for-windows-despite-lingering-critical-flaws.html

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I think Nature converted the

I think Nature converted the movie to mov. This will play with VLC.

Joined: 09/24/2012
Groups: Go Science
Preliminary questions

Science chat preliminary questions: do we ask our questions here before? Or on another place on the Forum?

Joined: 04/24/2014
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Answer!

Here's fine :) - but given there's a lot of opportunity to get questions lost, I'll be sure to start a thread today. :)

Here is that thread: http://fold.it/portal/node/2002801

Joined: 09/24/2012
Groups: Go Science
Player's supplementary material

Before or after the Science Chat: Would it be interesting that I share an abstracted version of the "story line" we Go Science shared to bkoep, with the explanation of what we did concretely to find this solution?

(I can already say that player's external to our group contributed to the result by exchanging ideas, photos, videos, PMs or recipes: namely Batz who joined the group and couldn't share his solo - he guided us with pictures and tips, then with hand fold on our group solution // susume who gave the good tips at the right moment rand exchanged with Batz on this particular puzzle// many writers of the recipes we used, including tvdl, Aliance Francophone team etc. // that's one of the many reason many "Foldit Players" co-authored this paper. I can reveal that pauldunn made most of the hand folding job, he explained it in our "story line".

Or would it be better to wait afterwards in order to help the chat focusing on the science part of this result?

(so my info here is that it will not be necessary to ask questions on the who and what, this might come later after the science chat).

Susume's picture
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Congratulations!

Congrats to Go Science and pauldunn on the winning solution! Very impressive result! I look forward to reading your story.

And congrats to the scientists on a very fine project and paper!

Joined: 09/24/2012
Groups: Go Science
Supplementary figure 10 in 3D without lenses !

It's amazing ! If you look at this picture and you squint until seeing 3 pictures instead of 2, you can see the central one in 3D !!!

jeff101's picture
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The Nature paper's Supplementary Information:

In http://www.nature.com/ncomms/2016/160916/ncomms12549/extref/ncomms12549-s1.pdf
Supplementary Figure 6 shows the distribution of Rosetta Energy scores.
On parts a & b of this figure, where would the given extended starting pose lie?
Is it in the big clump with Rosetta Energy around -200? What is the main
structural difference between poses with Rosetta Energy around -200 and
poses with Rosetta Energy around -1000?

jeff101's picture
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The Nature paper's Peer Review File:

http://www.nature.com/ncomms/2016/160916/ncomms12549/extref/ncomms12549-s3.pdf
seems to have 3 sections:

(1) 3 reviewers' critiques of the manuscript.

(2) Your responses to (1) above.

(3) 2 of the reviewers' responses to (2) above.

I am curious what the 3rd reviewer said in (3) above.

jeff101's picture
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The Nature paper's Fig.1:

The bottom right panel in the Nature paper's Fig.1 shows "a high-scoring solution in which the ordered regions of electron density were well fit by YPL067C". This solution has the Foldit score 11330.164.

Susume's picture
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Foldit score

Supplementary Figure 6 compares Rosetta score to Rfree, one of the criteria for selecting the best solution. The best Rfree solution (marked with a cross) falls between solos 4 and 5 in Rosetta score, which corresponds to a foldit score around 17700.

foldit score = 8000 + (-10 * Rosetta score)

jeff101's picture
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Rosetta Scores:

The formula Susume listed above
gives the following:

Foldit      Rosetta
score       score
------      -------
11330.164   -333.0164
17700       -970
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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons