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Recipe: Loop rebuild 6.0
Created by spvincent 42 52
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Name: Loop rebuild 6.0
ID: 100669
Created on: Sat, 02/07/2015 - 20:12
Updated on: Sat, 02/07/2015 - 20:12
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spvincent's picture
User offline. Last seen 2 days 8 hours ago. Offline
Joined: 12/07/2007
Groups: Contenders
Changes since 5.0 Quite a few

Changes since 5.0

Quite a few but two significant ones, designed to speed things up, particularly on design puzzles.

a) Removed the terminal wiggle in the Rebuild/Shake/Wiggle Loop.
b) Added a scoring mode (number 6) for puzzles with Slow Filters. When in this mode, Slow filters are mostly disabled but toggled on when determining the score.

For Design and Symmetry puzzles, drag the Score Type slider to the right so its at it's maximum value of 6: this will happen by default if it looks like the current puzzle has Slow Filters.

----------

Given a number of rebuilds, which is the best one to use? Not necessarily the best-scoring one, or even the best-scoring one at low CI (see http://proteinoftheday.wordpress.com ), but probably the best-scoring after shake and, which is what's going on here. Since Shake and Wiggle are computationally expensive, some effort is made to work only with the relevant sub-section of the protein.

Can be used at any Wiggle Power.

Algorithm outline


For each section to rebuild
   For each rebuild (defined by N Rebuilds)
      Rebuild once
      Set selection to that defined by Inner sphere
      Shake
   end
   
   For each pose corresponding to the two best scores above
      Set selection to that defined by Outer sphere
      Wiggle
   end

   Take the best pose from the two above
   Set selection to that defined by Outer sphere
   Shake (or Mutate if a design puzzle and that option chosen)
   Wiggle again if the Shake or Mutate gained anything.

   If we've gained an overall improvement
      Shake at low CI
      Wiggle at normal CI
      Record overall improvement
  end

end

Dialog settings

Rebuild Length

How big a section to rebuild. Values from 4 to 6 are typically most useful, but larger values are valuable

Min residue, Max residue

Only rebuild sections that lie within this range: by default the entire protein can be used. 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 loop you're working on.

Loops only

When set, only loops will be rebuilt, although a single non-loop residue is allowed. This effectively means that the end residue of a helix or sheet will be treated as a loop for rebuild purposes.

Convert to Loops

Meaningful if and only if Loops only above is unchecked. If checked, non-loops will be converted to loops before rebuilding: if not the secondary structure will be maintained.

So for example, if you had a helix from 35-40 and you wished to rebuild it as a helix with, say , a loop spacer 2 residues wide on either end, suitable settings would be:

Rebuild Length 10
Min residue 33
Max residue 42
Loops only unchecked
Convert to loops unchecked

N rebuilds

How many rebuilds to attempt. The default is a bit of a compromise: too small a value means that not enough poses will be created: too many and there's a high probability of ending up working on a pose which is extremely similar to the starting structure.

Mutate not shake

This checkbox will appear if and only if the puzzle contains mutable residues. If set (default), the sidechain shake in the algorithm will be replaced by a mutate.

Post wiggle threshold

An optimization used to prevent doing unnecessary shake/mutates. If the score after the best rebuild/shake (as described in the algorithm) is below the best by more than this amount, then skip the subsequent fuze-like processing as an overall gain is unlikely,

The default value works quite well: it might be worth lowering it to say 10 for endgame running or raising it to 60 or so at the beginning, particular for symmetry puzzles where overall scores are greater than usual.

Score type

Allows different scoring functions to be used - the values are:

1) Normal. Self-explanatory: the value as described by the program. Most of the time this is what you'll want

2) Exploration score. Perhaps one day there will be another exploration puzzle.

3) Energy score. Design puzzles without those filters.

4) Hiding. Just use the hiding component of the score.

5) Bonding. Just use the bonding component of the score.

In the last two cases, no fuzing will be done, irrespective of the threshold value.

6) As explained above: Toggles Slow Filters apart from scoring.

Check conditions met:

If set, check that conditions are met before accepting any improvement. For puzzles with RMSD conditions, etc.

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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