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Lab Report #28: A new tool for big problems
The Foldit team is preparing to test binder designs for the IL-2R target, and is developing a new Trim tool for tackling big protein problems.
NEWS
- Planned IL-2R binding experiment
- Sneak Peek at upcoming Trim tool
DESIGN OF THE MONTH
- A protein binder design by an anonymous player from Puzzle 2078: CD47 Binder Design. The binder has a complementary shape for hydrophobics on the target surface, and buried polar atoms are perfectly satisfied. Take a look for yourself in the January Design of the Month sandbox puzzle.
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 63 491 |
Tue, 12/21/2021 - 07:30 |
2 comments
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New Release!
Hey everyone,
We've just released a number of fixes and features to follow the recent interface release. Lots of stuff for bindable hotkeys, some help and tooltip clarity changes, and some crash fixes. We're working on addressing more of your feedback, so we'll be following this up more updates in the near future.
Release Notes:
- Allow action menu keyboard shortcuts to be rebound in the "Configure Keyboard Shortcuts" General Options submenu.
- Make sure that user-set keyboard shortcuts take priority over default shortcuts for other actions.
- To avoid conflicts with the actions menu, the default "Restore Very Best" and "Restore Credit Best" keyboard shortcuts were changed to Ctrl+B and Ctrl+C, respectively. These can be rebound in the "Configure Keyboard Shortcuts" General Options submenu.
- Made the "Configure Keyboard Shortcuts" dialog resizable.
- Clean up some residual keyboard shortcuts from the old interfaces & cross talk from other shortcuts. (e.g. Alt+T no longer invokes wiggle.)
- Add keyboard shortcuts for the side buttons (Help/Undo/View/Behavior/Cookbook). So as not to conflict with actions, these are F1/Alt+U/Alt+V/Alt-B/Alt+C by default. These can be rebound in the "Configure Keyboard Shortcuts" general options submenu
- Allow keyboard shortcuts to be bound to View Presets, including user defined presets (as with Recipes, these start off unbound.)
- Fix bug where the Color/View Protein/View Sidechains list in More View Options did not update when keyboard shortcuts were used.
- Add the screenshot and AlphaFold panel buttons to the list of rebindable keyboard shortcuts
- Other assorted hotkey-related bug and usability fixes.
- Update Help Menu.
- The puzzle timer tooltip has been updated to refresh more often to give an better display of the puzzle expiration.
- Puzzle timer in the scoreboard now displays minutes.
- Time abbreviations have been added.
- Address issue causing crash-on-exit bugs.
- Made small molecule design more robust to certain causes of crashes.
- Address crashes in scoring for ligand design puzzles.
- Fix bug in HBond Objective
- Fixed bug where the title wasn't resizing properly (leaving it and the objective panel as only three dots).
- The Secondary Structure action has been re-enabled for level "Folding Pathway I". This will allow players to complete it as intended.
- Adding clarity for Advanced Options buttons "Reset Roles" and "DELETE ALL OFFLINE PROGRESS"
- HBNets now show which atoms are incurring penalties.
- Added a 'grid' visualization that shows distances in angstroms.
As always, a big thank you to the devprev players for helping to test this release!
(Tue, 12/21/2021 - 07:25 | 1 comment)Last Office Hour of the Year!
Hey folks! Last Office Hour of the year happening this Tuesday, December 21st at 11 AM ET (Time Zone Converter). It will be led by beta_helix and Seth Cooper. They'll be focusing on new foldit tools! Looking forward to seeing y'all there!
(Sun, 12/19/2021 - 04:14 | 2 comments)IL-2R binders queued for testing
Following our series of IL-2R binder puzzles, we've selected 115 Foldit designs to test in the lab for binding to the IL-2R target. Read more in the Foldit blog!
(Thu, 12/16/2021 - 04:21 | 0 comments)
