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Recipe: Jolter 1.0
Created by spvincent 42 52
4.75
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Name: Jolter 1.0
ID: 101691
Created on: Thu, 12/17/2015 - 03:05
Updated on: Thu, 12/17/2015 - 03:05
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spvincent's picture
User offline. Last seen 3 days 18 hours ago. Offline
Joined: 12/07/2007
Groups: Contenders
Jolter is a rebuild script

Jolter is a rebuild script that's designed, as the name suggests, to jolt the protein out of a local minimum (that's the intent anyway), although it does seem useful in other circumstances. It successively rebuilds alternate structural elements in the protein, being prepared to accept a small loss in score after the usual quota of shakes and wiggles that normally follow a rebuild (gains are also accepted, needless to say).

The script never terminates: it's best run overnight or at least for a couple of hours. After cancelling the script you can start from the existing position, or, since the score meanders up and down when running the script. Suggested followup would be to run an Idealize script followed by the rebuilder of your choice.

Algorithm outline

Get list of secondary structure elements (helix, sheet, loop)

For each element (going alternately)
Repeat 8 times (value of N rebuilds below)
Rebuild element
Shake/Wiggle etc (Post Rebuild below)
end

Take best scoring position from above
If score is better than the current score minus the rejection threshhold then
make this the new current position
end
end

Min residue: max residue

Used to define the region of the protein to be rebuilt. Any secondary structure element that lies at least partially within this region will be processed. An element that contains a residue with a frozen backbone will not be processed.

N Rebuilds

How many times to rebuild each structure. Reducing this value may result in a more structurally diverse result, albeit at the likely expense of a poorer score.

Post Rebuild

The actions to be taken after each rebuild, The default is Shake/Wiggle/Shake/Wiggle (with nudges at low CI if things get stuck) but for design puzzles number 4 (Shake/Wiggle/Mutate/Wiggle) is likely preferable.

Rejection Threshold

Specifies how big a loss is permissible. The larger the value the greater the change in structure that will be allowed at the possiblee expense of score

Setting this to zero means that only gains will be permitted: useful in the earlier stages.

Helix spacer, Sheet spacer, Loop spacer

When rebuilding, specifies the length of a spacer at either end of the structural element that will be included in the rebuild. So if the value of Helix spacer were 3, then when working on a helix from 63 to 75, the actual rebuild length would be 60 to 78.

Score type

If set to 2, toggles filters off except when determining the score. For better performance on slow design puzzles.

Joined: 03/15/2016
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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