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Recipe: Helix Rebuild 2
Created by spvincent 47 31
Your rating: None Average: 4.3 (53 votes)


Name: Helix Rebuild 2
ID: 45788
Created on: Thu, 03/21/2013 - 00:21
Updated on: Thu, 03/21/2013 - 00:21

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spvincent's picture
User offline. Last seen 6 hours 16 min ago. Offline
Joined: 12/07/2007
Groups: Contenders

This script is probably most usefully used in the early/middle game (although the chess analogy can be pushed too far).

Algorithm outline

For each helix, bracket it with a loop on either end, rebuild it and the loop spacers several times at low CI, take the highest scoring result and then do Shake, Wiggle, Shake, nudging the protein slightly if the wiggle gets stuck. If the score is reasonably close to the best score, do a Fuze.

Loop spacer

The length of the loops at either end of the helix are to be. The greater the value, the more freedom there is for the helix to adopt new configurations but the less likely you are to get local refinement.

Helix list

A list of check boxes showing the helices in the protein.


If checked, all selected helices will be rebuilt together. this setting was intended for the case where there were two antiparallel helices that might beneficially be rebuilt together but I've yet to see a case where it produces a gain.

Number of rebuilds

How many times to rebuild the helix before Shaking, etc.

Clash Importance

The CI during rebuild

Fuze Threshold

How many points within the original score before attempting a Fuze

Mutate not Shake

For design puzzles only: If set does a Mutate rather a Shake (i.e. does Shake/Wiggle/Mutate)

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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, RosettaCommons