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Science Chat Transcript

Thanks to everyone who joined yesterday's Science Chat! A transcript of the chat is available here.

Also, the Siegel lab got back to us with a quick update on the aflatoxin project. They ran into some problems with the previous designs, but they are preparing a new approach and we expect to have more aflatoxin puzzles in the coming months!

From the Siegel lab:
After ~500 designs tested and 0 hits we started to get worried about some core hypothesis/assumptions we were making. So we went back and did a more detailed study on the thermodynamics and kinetics of base catalyzed ring opening and closing and we found some very surprising and unexpected results. Normally lactones favor cyclization at low pH and the open form at neutral or high pH….. well, aflatoxin is different. Turns out it is more stable in the closed form than the open form all the way until pH 9!!! Lots of interesting theories here about evolution and why that is… but long story short… we’ve been trying to break a law of thermodynamics!

So for now we took a step back and are moving to an entirely new class of enzymes and reactions. The plan is to get a baseline of genes there like we did for the lactonases, figure out which express the best, have the best structural information, and functional plasticity. Then get models in place so we can start posting new design puzzles. We are hoping the first design puzzles will be up in ~2-3 months depending on how smoothly the initial gene analysis phase goes (~20 genes with structures or close homologs are identified, ordered, and on their way).

Hope this helps, and sorry for the radio silence. We have been completely taken surprise by the aflatoxin thermodynamics. But if it hadn’t been for the player designs (many looked great and worked on other substrates) I am not sure we would have realized to go back and look at this fundamental assumption!

(Thu, 04/11/2019 - 18:38  |  0 comments)

Developer Preview Release Soon

Hey everyone,

We're about to release an update to the developer preview with the following fixes and changes:

General:
* Certain puzzles may now have some filters only applied to part of the protein (such as designing binders).

Bug Fixes:
* Fixed a minimization issue on Mac.
* Fixed a handle leak on Windows.
* Links to the new wiki should once again work.
* Fixed a number of threading issues that may have been causing hangs or crashes.
* Fixed a crash when stopping Pick Sidechains.

(Mon, 04/08/2019 - 23:06  |  0 comments)

Spring 2019 Science Chat!

Science Chat April 10th in veteran chat

Join the Foldit team for a chat about the science behind recent Foldit puzzles! If you leave questions in the comments below, we can prepare some answers in advance to help move the discussion along!

Date: Wednesday, April 10th, 2019
Time: 9pm GMT; 1pm Pacific Time Zone
Location: #veteran chat

http://www.thetimezoneconverter.com/

(Thu, 04/04/2019 - 18:18  |  10 comments)

Submit cover art for accepted Foldit paper!

The research paper we recently drafted has been accepted for publication in a scientific journal! The paper reports the protein design work of Foldit players from the past 6 years, and will be published in the coming weeks.

Scientific journals like to print each issue with a unique cover, usually with flashy art that describes some of the research in the issue. We'd like to submit artwork that could be used on the journal cover when our paper is published, and we want your help!

If you have an idea for a journal cover related to protein design in Foldit, please share it with us! The ideal artwork should be eye-catching, and communicate relevant themes like citizen science, protein design, creativity, and/or computer games. Please send us any art, as a high-resolution image file, to foldit.publications@gmail.com before April 3 at 23:59 GMT.

Since the journal only allows a handful of submissions, the Foldit team will select favorites to be submitted to the journal as possible cover art.

(Wed, 03/27/2019 - 22:34  |  12 comments)

Veterans Needed: Show Us Your Skills

Hey veterans,

This is a request for help from anyone interested in the design of Foldit as a game.

As a game scientist, I am trying to understand how Foldit requires particular skills from you as a player, and trains you in those skills. Skills in this sense are discrete, atomic ideas that the player builds up to larger strategies. For background on this, please read Dan Cook's article on the chemistry of game design.

My mission for you, should you choose to accept it, is to design what Foldit's skill "tree" would look like. What are Foldit's atomic skills, and how do they combine to create the larger strategies that difficult puzzles demand of you?

Dan Cook gives an example of a skill tree here, this one about the basics of Tetris. I've also made a small example about the basics of Mario.

You can make your own skill tree using draw.io. When you've finished drawing your skill tree, please send it to me (joshmiller) in a private message.

Your help in designing this skill tree will be hugely valuable to research on Foldit and citizen science games broadly. Thank you so much for taking the time to help with this project. I am excited to see what you create, and even more excited at the potential that these trees may be used in the future development of Foldit!

(Thu, 03/14/2019 - 14:55  |  6 comments)
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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, Amazon, Microsoft, Adobe, RosettaCommons