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New Update in 'Experimental' Update Group!

As many of you are probably aware, Rosetta is the "science engine" behind Foldit. It's been about two years since we last updated the version of Rosetta that Foldit uses under the hood. Since then, there have been many developments and improvements in Rosetta, and we thought it's time to update again.

Here's just a sampling of some of the improvements that come with the updated Rosetta:

* Fixes to some of the random crashes on MacOS
* Fixes to electron density-related crashes on Linux
* Fixes to symmetry-related crashes on all platforms
* Better support for non-protein residues, such as RNA, carbohydrates, lipids and non-canonical amino acids
* Support for modeling membrane proteins
* Improved detection of native-like hydrogen bonding networks

But perhaps the biggest change that comes with the update is improvements to scoring. There's been a *lot* of work put into the Rosetta scoring function recently, and just about every portion of scoring has been re-evaluated and re-optimized. (For those who want a nitty-gritty breakdown of the changes, a comprehensive overview has been published, along with details on how things were optimized.)

Here's a demonstration of the improvement. When looking at the ability to discriminate native-like proteins from non-native-like ones, for many proteins the new scoring function is able to do a much better job than the older scoring function:

(Park et al. J. Chem. Theory Comput., 2016 DOI: 10.1021/acs.jctc.6b00819)

Here each red point represents a structure prediction run for a different protein. The discrimination ability of the two scoring functions are plotted, using a metric where 0.0 represents no discrimination between native-like and non-native, and 1.0 represents ideal discrimination. The diagonal line represents no difference between the two scoring functions, and any points above the diagonal line represent proteins where the new scoring function does a better job than the old one.

This also is reflected in the score-versus-rmsd "funnel" plots for the predictions, where the new scoring function does a better job of eliminating false minima (blue) than the older score function does. (In these plots, better scoring structures are lower on the y-axis, and more native-like structures are further to the left. Eliminating false minima means a selection of top-scoring structures is less likely to include non-native-like ones.)

(Park et al. J. Chem. Theory Comput., 2016 DOI: 10.1021/acs.jctc.6b00819)

This improvement isn't limited only to protein structure prediction. The new scoring function shows discrimination improvements in a wide range of protein prediction problems, including protein-protein and protein-small-molecule interaction predictions.

(Park et al. J. Chem. Theory Comput., 2016 DOI: 10.1021/acs.jctc.6b00819)

There is a slight drawback to these improvements, though. The new scoring function is slower than the current one. (In our tests, it averages about 30% slower.) We don't anticipate this being noticeable in general interactive use, but it may affect things like long-running shakes and wiggles. Most affected will be scripts which use a set number of iterations of shake and wiggle - these will run for longer, and if you've optimized the number of iterations for the current scoring function, the optimal number of iterations may have changed in the new one.

We're excited about these score function improvements, though, and think the better results are worth the slowdown. You might spend a bit more time working on a single structure, but you should hopefully spend much less time working on "bad" or "scientifically uninteresting" structures.

So, if you're feeling adventurous, please help us out by testing the updated version. To do this, switch your update group to `experimental`. In addition to testing how the slowdown affects scripts, we also want to make sure no bugs have slipped in on how the various tools behave. -- Note that, due to the difference in scoring, the puzzles available with `experimental` are not the same as with the `main` and `devprev` clients. If you want to play the regular Foldit puzzles, you'll need to switch your update group back to 'main'. None of the 'experimental' puzzles will count towards your website rank, but they will help us work out any issues prior to releasing it to the general public!

( Posted by  rmoretti 78 1205  |  Thu, 02/08/2018 - 21:42  |  1 comment )

Player Feedback on the Menus Welcome

Hello all! Hope that you all are having a wonderful start to this fine February.

We are looking for feedback on the current menus from you, our wonderfully dedicated players. If you feel so inclined to give your opinion, we would absolutely welcome it. You can find our menu survey here. All responses are anonymous and you do not need a Google account to log in. Additionally, feel free to shoot me a message if you have any questions or concerns.

(Wed, 02/07/2018 - 19:13  |  0 comments)

New electron density for Foldit-designed protein!

We’ve been able to crystallize another protein design from a Foldit player, and have derived an electron density map at 1.9 Å resolution!!! Check out Puzzle 1475 now, and see if you can fold the protein into the electron density map!

(Thu, 01/25/2018 - 23:19  |  2 comments)

Updates from the Foldit Team - December 2017

Here are some things the Foldit team has been working on lately:

  • rmoretti: Bugfixes and interface improvements for drug design puzzles; updating the underlying Rosetta code to include the most recent improvements.
  • joshmiller: Making the Conditions system more user-friendly and working on putting it in some of the tutorial levels as sort of "side quests" which will earn bonus points.
  • bkoep: Trying to crystallize more proteins in the lab.
  • jflat: Fixing that darn IRC server.

UPDATES DISCLAIMER: We want to keep the community apprised of what we are working on, but please note that not everything we spend time on will necessarily come to fruition quickly or even at all. The nature of research is nebulous and often there is no clear answer to a problem. Researchers can work on something for a long time and end up without usable results. Also please keep in mind that we are working on projects that the team has deemed the most appropriate/valuable use of our time and resources based on the information we have at hand. This may not jive with what all players feel is the best for Foldit and while we are certainly willing to listen to your concerns, please understand this may not change our direction. We value, put weight on, and appreciate your feedback nonetheless.

(Wed, 12/27/2017 - 23:47  |  0 comments)

New Release!

Hey everyone,

We've just released a new update. The following features and fixes have been added:

* Increased the band strength upper limit.
* Added lua script functions for adjusting the wiggle power.
---behavior.GetWigglePower() - will return a string with value 'l' (low), 'm' (medium), 'h' (high), or 'a' (auto) for the current value of the wiggle power.
---behavior.SetWigglePower(string power) - will set the wiggle power based on the values above.
---behavior.HighPowerAllowed() - will return whether high power wiggle is allowed on this puzzle.

Bug Fixes:
* Various fixes for RNA support. A number of tools have been disabled. Shake should be available in the Selection Interface, and should only run on the selection. Rotamer cycling with the arrow keys should work correctly for RNA.

As always, a big thanks to your devprev testers for helping to test this release!

(Fri, 12/22/2017 - 00:27  |  0 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, Microsoft, Adobe, RosettaCommons