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Recipe: ST - #0-Rebuilder Group 1 - with mini Rosetta energy
Created by Seagat2011 83 1564
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Name: ST - #0-Rebuilder Group 1 - with mini Rosetta energy
ID: 29324
Created on: Mon, 06/06/2011 - 13:43
Updated on: Tue, 06/14/2011 - 08:17
Description:

Requires User-specified rebuild range. QSlots (1-10) are used. Quickly scores a rebuild for stabilization/rejection, based on compactness, hiding, clashing, and disulfide bridges. recommended for all Puzzles ( Exploration, Design, Multi-start, Freestyle ) + combinations, thereof. Press Ctrl+N to restore best score, and Ctrl+1 to restore your best template.



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Joined: 08/24/2010
Hi

The idea behind this recipe is most rebuild recipes are random (they don't take into account the long-term viability during a rebuild), this dramatically increases the running-time; so the idea of incorporating mini Rosetta is to finally be able to spot a good rebuild.

rebuild-stops which DO NOT improve the mini Rosetta energy score are rejected.

Scenario:

If my starting mini Rosetta energy is 1052.012 / 20906, then a rebuild which lowers this score is seen as (long-term) undesirable and is rejected (the rebuild will not be assigned a stabilization saveslot):

Stabilized score = 8052.012
mini Rosetta = 1052 / 20906
Template = -4012.800

rebuild-stop #1
Pre-Stabilized score = -912.812
mini Rosetta = 952 / 20906
Status: Rejected

rebuild-stop #2
Pre-Stabilized score = -10112.812
mini Rosetta = 9052 / 20906
Status: Accepted -- This rebuild-stop will be assigned to a saveslot

USER-SPECIFIED PARAMETERS

i = 12 -- Start index ( idx )
offset = 26 -- offset ( Note: idx2 = idx + offset )
duration = 3 -- rebuild duration. Helix (3), Loop (2), Sheet (4)

Note: when rebuilding helices (H) or sheets (S), it is recommended "idx" and "offset" end at a loop (L) structure.

Example:

1-2-3-4-5-6-7-8-9
L-L-H-H-H-H-H-L-L

..in this example, it is recommended idx = 2 , and offset = 6.

REFERENCES

1. Rosetta 3.0 User-guide - http://www.rosettacommons.org/manuals/rosetta3_user_guide/index.html
2. Rosetta 3.0 Potential Energy Equation - http://www.rosettacommons.org/
3. The Baker Laboratory - http://depts.washington.edu/bakerpg/drupal/
4. Recipe: ST - mini Rosetta energy model - http://fold.it/portal/recipe/28823
5. Recipe: #0 - Rebuilder Group 1 - http://fold.it/portal/recipe/23682

Joined: 08/24/2010
**Updated - June 10 2011**

**Updated**

bugfix: If more than 15 rebuild-rejections, 0-rebuilder group 1 successfully makes the detection and continues with recipe.

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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