Fragment Filter and the Remix Tool

Hey everyone,

Foldit designs have come quite a long way, but there are several issues that we're still seeing in player-generated models.

One of the biggest problems is that some regions (primarily loops) in your models don't match the shape of regions in known natives. Since some shapes are more common than others, this means that these shapes are less statistically likely, and have a reduced probability to fold up in practice.

With that in mind, we've created...

The Fragment Filter!

So first - What is a fragment? A fragment is a shape for a small region of the protein. Imagine a loop of 8 residues. Loops can have drastically different shapes, and each of these shapes is a fragment of size 8.

The Fragment Filter tells you when part of your protein has an unrealistic fragment.

It does this by marching through the protein, looking at every fragment of size 4 (overlapping). For each of these fragments, it does a look-up into a database of known fragments that have been generated from a set of natives. If it cant find any fragments with shapes similar to the one you have in your protein, you'll get a score penalty, and it will highlight the fragment as a bad fragment.


The bad fragment is shown by the glowing red residues.

In this way, we ensure that the models you are generating are composed of statistically likely fragments, increasing the probability that they will fold up in the lab (and therefore the probability that we will test your design!).

From our analysis, top Foldit design solutions usually have 1-3 of these bad fragments.

So if your design has a bad fragment... how do you fix it?

The Remix Tool

Remix changes the shape of the selected region to match a 'good' fragment.

There are a couple of basic steps to using the Remix tool:

1. Select the region to remix.

Remix will work on selections of size 4-10. Even if there are only 4 bad residues, you can try larger sizes to try to get better results out of Remix. Just make sure the bad fragment is included in the Remixed region.


Here we've selected the bad fragment. In the Classic interface, Remix will work on secondary structure.


The Remix button will pop up when you select regions of size 4-10.

2. Remix the region!

When you hit Remix, the tool will do a lookup into a database and find a shape that has the same size and similar endpoints. Then it copies this shape onto your protein.

Remix wont always find something to copy (though it usually does), so you might have try selecting a different region, or modify the one you have until it finds something.


By using Remix, we've fixed the bad fragment, but this has created issues in the rest of the protein.

3. Resolve the resulting issues.

Similar to the Idealize tool, using Remix will create global changes even though you're just modifying a local area. This can cause issues elsewhere in the protein that you'll have to fix.

One way to fix them is to use low clashing importance and bands to stabilize the structure.

Another option (my favorite) is to insert a cut near one end of the region before Remixing, and then wiggle that region after Remixing until the cut can be closed. This prevents the global changes from ever happening, and usually works pretty well!


By using other game tools, we can bring the structure closer to its original shape, without the bad fragment.



Remember that you can fix the bad fragments any way that you want - Remix might just make it easier. It will be available on any puzzle that uses the Fragment Filter.

Like always, we'd love any feedback that you have on both the Fragment Filter and the Remix tool.

( Posted by  jflat06 92 730  |  Wed, 11/13/2013 - 22:02  |  5 comments )
2
Joined: 02/08/2012
Groups: None
A possible reason for our bad fragments

It may be possible that players simply don't have enough time to work on things.

jflat06's picture
User offline. Last seen 5 days 13 hours ago. Offline
Joined: 09/29/2010
Groups: Window Group
.

That could be, but the most likely culprit is that the score function simply does not encode the necessary information to prevent these bad fragments from occurring.

Bad fragments can score well in Foldit score, so people don't have any reason to not build them (competitively), or any indication that they've even done something wrong.

spmm's picture
User offline. Last seen 10 weeks 4 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
using in selection interface

The buttons across the bottom of the screen are now just disappearing off to the right on a standard monitor size.

However remix does have a hot key number (4)

If you deselect everything and apply bands the usual remove and disable bands buttons come up (hence the rightward push)

If you select something and then apply bands the two band buttons do not appear.

Also it would be better if the disable bands button didn't move to the end of the row, (this for some reason is standard behaviour) it should remain under your cursor so you can switch it on and off as a script is running.
Not a biggie.

bertro's picture
User offline. Last seen 12 hours 17 min ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
also in selection interface

totally agree with spmm

wisky's picture
User offline. Last seen 5 weeks 6 days ago. Offline
Joined: 07/13/2011
I would personally like to

I would personally like to see more puzzles with the Fragment Filter/Remix tool on them, it doesn't seem to slow down the game too much :)

It will be interesting to see how this actually affects the protein's fold in the end...

Get Started: Download
  Windows    OSX    Linux  
Windows
(7/8/10)
OSX
(10.7 or later)
Linux
(64-bit)

Are you new to Foldit? Click here.

Are you a student? Click here.

Are you an educator? Click here.
Search
Only search fold.it
Recommend Foldit
User login
Soloists
Evolvers
Groups
Topics
Top New Users
Sitemap

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