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Recipe: Helix Rebuild V2 1.0
Created by spvincent 33 32
3.25
Your rating: None Average: 3.3 (4 votes)

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Name: Helix Rebuild V2 1.0
ID: 40280
Created on: Mon, 04/02/2012 - 17:49
Updated on: Tue, 04/03/2012 - 00:49
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spvincent's picture
User offline. Last seen 5 hours 59 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Helix rebuilding is probably

Helix rebuilding is probably best done by eyeballing but this script can be used instead: probably best used as a middle game script.

This script brackets each helix with a loop on either end, rebuilds it once, and then does a Shake, Wiggle, Shake, Wiggle, nudging the protein slightly if a wiggle gets stuck. If this results in a new high score all well and good. If not it may still be a useful candidate for further investigation as the script doesn't do any fusing. The best result that comes closest to the highest score is stored in Quicksave slot 10 (changeable to any other number). After terminating the script and if the score hasn't improved, it's recommended that you load the result in Quicksave 10, unfreeze it (the rebuilt area will be bracketed with frozen segments to identify the helix that was rebuilt, and try a fuze 9or something else.

Loop spacer: a value of 2 seems to give decent results: larger values will mean greater structural changes.

Min residue, Max residue. By default it does the whole protein but these values can be modified to only rebuild helices within a certain range.

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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