Back to Recipes Homepage
recipe picture
Recipe: Loop Remix 11.0
Created by spvincent 24 15
5
Your rating: None Average: 5 (9 votes)

Profile

Name: Loop Remix 11.0
ID: 104760
Created on: Wed, 04/21/2021 - 20:08
Updated on: Thu, 04/22/2021 - 03:08
Description:

See first comment



Best For


Comments

spvincent's picture
User offline. Last seen 2 hours 56 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Loop Remix 10 is intended as

Loop Remix 10 is intended as a replacement for Loop Rebuild. It no longer supports Rebuild and has been significantly simplified: a lot of obsolete functionality has been removed. At least I hope it's obsolete and Foldit doesn't suddenly reintroduce old features. It's oriented towards design puzzles.

The default settings work pretty well early: later on in the middle/late game the Remix Criterion slider can be set to 4 to make sure all possible sections are processed: it might be worth converting to loops too.

One thing that has changed in the algorithm is that the old Loop Rebuild attempted to pick the most likely remixes to succeed by doing a shake after each remix and selecting the two top-scoring solutions to wiggle after which the highest scoring pose only would be used for subsequent processing. This is a bad way of doing it: its very hard to judge that early how well a particular remix will turn out. This version doesn't attempt to short-circuit processing until the very end when it does a mini-Local Mutate if the score is close enough to the pre-remix score.

Algorithm outline


For each section to remix
   Remix ( N Remixes) times
   For each remix
      Shake
      Wiggle
      Mutate
      Wiggle
      If Mutate gained something but Wiggle didn't
         Nudge (Wiggle at low CI: Wiggle at CI 1.0)
      If we're close enough to the current best solution 
         Do a mini-Local Mutate centred around the section midpoint
         If there's an overall improvement accept it and go onto the next section.
   end
   

end

Remix Length

How big a section to remix. Its probably best to leave this at 4 since design puzzles are normally built up from Idealized elements.

Min residue, Max residue

Only remix sections that lie within this range: the default setting is the entire protein with terminal locked residues trimmed off. These values can be usefully changed to whatever region of the protein you're working on: it's often desirable to set them to the start and end of a region you're working on.

N remixes

Probably best left at 4: might be reduced if anything.

Remix criterion

Slider with 4 values that controls, within the range defined above, which sections will get rebuilt based on their secondary structure.

1) Loops only
2) Loops allowing one non-loop residue.
3) Loops or sheets (no more than one helix residue)
4) Anything

Local mutate threshold

Defines how close scorewise we have to be before doing the final Local Mutate. The default is set at 80 which is plenty unless you happen to get a big gain in filters.

Keep bands enabled

If false, disables bands and reenables them on script termination.

Filters off for wiggle

In the interests of performance.

Test for stability

On recording a gain, attempt to determine whether the resultant pose is stable by turning off filters, wiggling, and then turning filters back on again to see if the gain still holds.

Verbose

Prints extra info about progress

Want to try?
Add to Cookbook!
To download recipes to your cookbook, you need to have the game client running.
Parent

none

Children

none

Authors
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