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Recipe: Loop rebuild 5.4
Created by spvincent 41 13
Your rating: None Average: 4.5 (50 votes)


Name: Loop rebuild 5.4
ID: 49363
Created on: Wed, 06/11/2014 - 08:44
Updated on: Wed, 06/11/2014 - 15:44

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Best For


Joined: 12/07/2007
Groups: Contenders
Changes since 5.2 1) Added

Changes since 5.2

1) Added threshold value for post-rebuild threshold improvements at low CI.
2) Alternate score functions


The default settings work pretty well if you don't want to be bothered reading this.

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 ), or the best -scoring after shake, but probably the best-scoring after shake and wiggle, which is what's going on here. Since Shake and wiggle are computationally expensive, considerable effort is made to work only with the relevant sub-section of the protein.

Tested and best used at Auto WP.

Algorithm outline

For each section to rebuild
   For each rebuild (defined by N Rebuilds)
      Rebuild once
      Set selection to that defined by Inner sphere
      Wiggle for a fixed number of iterations
   For each pose corresponding to the two best scores above
      Set selection to that defined by Outer sphere
      Wiggle adaptively in the NC-approved way

   Take the best pose from the two above

   if initial score minus current score is less than threshold value
      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.
      Wiggle at low CI

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


Dialog settings

Rebuild Length

How big a section to rebuild. Values from 4 to 6 are typically most useful.

Min residue, Max residue

The range to be rebuilt: by default the entire protein. 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 nnly 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

Number of 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, the side chain wiggle 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/wiggle (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 yo 60 or aso at the beginning, particular for dimer 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. Oerhaps 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.

Check conditions met

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


After each rebuild sequence, up to three numbers are printed.

The first is the difference between the starting score and the best score after a rebuild/shake/wiggle sequence.

The second, which will only be shown if the number above plus the threshold value is greater than zero, shows the gain from the subsequent Shake/Wiggle/Wiggle at Low CI/Wiggle
sequence. Watching this value provides a clue as to what value to set the threshold slider: ideally the slider should be set to the maximum likely gain value .

The third, which will only be shown if the previous processes resulted in an overall gain, is the gain from doing the final Shake at low CI/Wiggle sequence.

Joined: 09/24/2012
Groups: Go Science
thanks for the excellent explanation

The strategy seems promizing. I'll try the recipe asap.

Joined: 04/11/2013
Yes Thanks sp :)

Yes Thanks sp :)

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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, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons