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Recipe: Loop explorer 1.0
Created by spvincent 39 34
4.5
Your rating: None Average: 4.5 (6 votes)

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Name: Loop explorer 1.0
ID: 44410
Created on: Wed, 10/24/2012 - 21:23
Updated on: Wed, 10/24/2012 - 21:23
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spvincent's picture
User offline. Last seen 1 day 18 hours ago. Offline
Joined: 12/07/2007
Groups: Contenders
Description

Repeatedly rebuilds, shakes and wiggles a selected area, storing the most promising results in Quicksave slots.

This script is not intended to improve your score in itself, although it may have that happy side effect. Its intended use is as a late game script to explore new configurations of an existing loop,which can then be loaded, inspected, and the rebuilder of your choice used to hammer away at the new loop and hopefully produce a better score.

Min residue: max residue

Used to define the area (not necessarily a loop, despite the name of the script) to be rebuilt. A likely candidate would be one 8-12 residues in length with an appearance that displeases you or which you have cause to think may be stuck in a local minimum.

Weight according to difference

If unchecked, new configurations are saved according to best score in two Quicksave slots (11 and 12 by default). If checked a weighting function (based on differences between the position of each side chain between the new configuration and the original) is applied such that new configurations that are significantly different from the original will be preferred, even though their score may be lower.

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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