Sneak Peak - The Trim Tool

We wanted to give players a sneak peek at an exciting development project that is currently in progress.

The Foldit team is always looking for ways to allow players to tackle new types of problems. One of the biggest obstacles we run into when trying to design a new puzzle is protein size. Many potential puzzles never get past the planning phase because they simply contain too many residues.

Currently, Foldit can only handle a little over a hundred residues before the interface and tools start grinding to a halt - especially on lower spec machines. In some instances, we have run puzzles with more residues than this, but we’re still limited to a few hundred in the best of situations. We’re always torn between providing you with the latest interesting challenge while also trying to keep the client responsive.

In an upcoming release, users will be able to try out a feature that has been designed to help solve this issue: the Trim tool (name is a work in progress!).

The Trim tool, along with the corresponding Untrim tool, will allow Foldit users to focus on specific regions of a protein in isolation, as if these regions are their own, smaller puzzles.

With the use of the new selection UI, users can select any region—or set of regions in a puzzle—and then click on the Trim button in order to create a new structure containing only the residues that had been selected.

After operating on this trimmed structure with all of the features normally available for a Foldit puzzle, users will be able to introduce the changes to this region back into the full puzzle, using the Untrim button.

We hope you have enjoyed this feature preview! We are still solving technical challenges and finalizing the behavior of the Trim tool, but we hope to release it in early 2022. We are already excited about the potential of this new set of tools, and look forward to seeing what Foldit players can do with them!

( Posted by  jflat06 60 552  |  Tue, 12/21/2021 - 07:30  |  2 comments )
Joined: 12/06/2008
Groups: Contenders
Much needed.

I'm intrigued about the possibility of working on larger proteins.

One challenge is going to be how you would re-integrate a trimmed section back into the rest of the protein after one does a major rebuild which significantly relocates the trimmed ends. The Cut tool won't let you rejoin ends until they are close together.

I also imagine it being a challenge to display a correct score. Is the trimmed area still interacting with the rest of the protein? The video clips you show above imply not.

bkoep's picture
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Joined: 11/15/2012
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Astute concerns

Yes, these are two of the biggest challenges facing the implementation of the Trim tool.

By default, the trimmed endpoints will be constrained to their original coordinates. This will ensure that the backbone of the trimmed region can be easily and seamlessly spliced back into the complete model. Users can insert their own cutpoints if they would like to work with free ends, but these user cutpoints would still need to be closed manually later on.

The trimmed area is not interacting with the rest of the protein. This is unfortunately necessary to achieve the boost in Foldit performance, since the typical Foldit slowdown arises from both the rendering and scoring of many residues. This means it will be possible to inadvertently create new clashes between the trimmed section and the excised sections, if you are not careful. Some "touching up" may be required when restoring the complete model.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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