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This is the official question thread our next Science Chat, and this paper of course, will be the main theme (but other science questions for Foldit are welcome).

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!

Please be sure to put your questions below.

Susume's picture
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Rosetta score

Is the structure published in the PDB (pdb 5KCI) taken directly from a foldit solution, or was additional processing applied? What was the Rosetta score of the foldit solution that was selected for publication in the PDB?

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Did Puzzle 1193 results go into the Nature paper?

Puzzle 1193: UMich Challenge: Refined Density
(http://fold.it/portal/node/2002056)
is related to
Puzzle 1152: Foldit vs. UMich Electron Density Challenge
(http://fold.it/portal/node/2001344)

Did any results from Puzzle 1193 go into the Nature paper
discussed at http://fold.it/portal/node/2002791 ?

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U of M challenge result

Is replication not a concern?

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What about the full structure? (incl. unordered)

The Foldit better matched the density after removing the unordered segments.

What about refining these unordered segments?

1) Arent' they important for the full function of the protein?
2) Are these segments part of the (before competition) published structure? and where them there correct?

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How did you sample the pictures for the movie?

The beginning of the movie is understandable (it's the main hand fold part).

At the end, it's like seeing a DRW working in accelerated.

Do you have a track of all the moves of all the solutions?

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Supplementary Figure 3 (1 remark & 1 question)

[I suppose that a command counted as unique (thus not multiplied by the number of iterations)?]

=======================================================================
It's quite interesting to see that "pure hand manipulations" (rigid body, tweak and pull) represent only about 3.26% of the moves while this is the most strategic part of folding, as seen in the movie.

Optimization tools (including in recipes) represent about 97% of the moves
=======================================================================

1) What is the share hand/tools for Trained crystallographers?

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HTC1 and drug induced psychiatric diseases

Supplementary note 2: "this highly conserved channel is the most likely α - synuclein binding site".

Butler et al (2016), Dopamine Transporter Activity Is Modulated by α-Synuclein:

"α-Synuclein is implicated in neurodegenerative disease and drug addiction."

"Understanding the mechanisms associated with α-synuclein regulation of DAT may reveal disease-modifying targets for the treatment of pathologies associated with DA dysregulation."

HTC1 is quite a great discovery !

Question: How did you know α-Synuclein was a good candidate for this HTC1 conserved channel?

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oops the answer is in the paper

sorry, the answer is in your reference 10 (the reason you choose this protein) ...

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Are foldit designs better?

Have foldit designs gotten more realistic since the Ideal Loop filter was introduced? Are any being produced for lab testing?

What problems remain with the designs you are seeing now?

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Nature

The Nature communication was published online. Will it ever be published in hard copy?

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Recent denovo puzzles

I've noticed that the recent denovo puzzles look like they were designed in foldit (possibly by foldit players). Can you confirm this? Also can you comment on how the designs were chosen and on what you hope to learn from posting these puzzles?

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Are helices made by ideal SS really ideal?

I'm curious to get an answer to this forum post: http://fold.it/portal/node/2002580

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HTC1 and drug induced psychiatric diseases (reset)

Supplementary note 2: "this highly conserved channel is the most likely α - synuclein binding site".

α - synuclein is a Human protein.

Butler et al (2016), Dopamine Transporter Activity Is Modulated by α-Synuclein:

"α-Synuclein is implicated in neurodegenerative disease and drug addiction."

"Understanding the mechanisms associated with α-synuclein regulation of DAT may reveal disease-modifying targets for the treatment of pathologies associated with DA dysregulation."

Question:

YPL067C being a yeast protein, what do you expect with this discovery?
-could researchers then find similar Human HTCs that regulate DTA?
-is YPL067C a toxical and/or a potential drug?

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