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Recipe: Quaking Rebuild 2.0 filter
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Name: Quaking Rebuild 2.0 filter
ID: 48072
Created on: Wed, 02/05/2014 - 12:27
Updated on: Sun, 02/01/2015 - 12:57

Loop Rebuild modified so that after Rebuild/Shake/Wiggle etc: it performs some Local Quakes rather than Fuses in an attempt to improve the score.

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Joined: 09/24/2012
Groups: Go Science
Adapted to New Chapter + dialogs including tvdl "WORKON" module

New to version 2.0:

1-optimized for New Chapter
2-added dialogs (defaults are what I prefer)
3-strong to adress all types puzzles (ligands, locked etc)
4-tvdl Dialog to select where to work on: Loops, Helixes, Sheets, add on segment before and after zones (good for small loops), + your own zone of the protein you want to select.
5-From zone length big to small (because there are less ocurences of big zones than small ones, you'll fast be on smaller ones)
6-This is automatically adjusted if zones selected are too small (e.g. "only loops" but there are only small loops)

7-Advanced easy editing options to be edited in the code
7a-default "loops with one non loop" is easy to edit, so that you can easily make a copy of the recipe with the default you prefer, e.g. "Only loop" or "All, helixes or sheets will be converted to loops".
7b-tvdl Dialog to select where to work on can quite easily be extended to more choice by editing the recipe: all possibilities to select are embedded in the tvdl module.
7c-I added to the generic tvdl module a function to add segments before and after the zones

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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