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Recipe: Loop rebuild 3
Created by spvincent 40 22
Your rating: None Average: 4.5 (74 votes)


Name: Loop rebuild 3
ID: 41540
Created on: Fri, 05/11/2012 - 12:09
Updated on: Fri, 05/11/2012 - 19:09

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spvincent's picture
User offline. Last seen 3 hours 23 min ago. Offline
Joined: 12/07/2007
Groups: Contenders

Changes since 2.0

The principle change from previous versions is that the script selects the best rebuild in a different way. Rather than selecting the best scoring solution from a number of rebuilds, it takes the best score from the same number of rebuild/shakes. While this is likely to give a "better" rebuilt structure in the sense that it is more likely to result in a score improvement, there's considerable overhead in doing shakes so it will look at fewer structures than previously in the same amount of time.

It's not necessarily clear this is an improvement on earlier versions of this script. My impression, unconfirmed by comparative testing, is that it is better for rebuild lengths of 6 or more, not so good for 4 or fewer, and for rebuild lengths of 5 it's probably a wash.

Algorithm outline

1) Pick a section to rebuild
2) For how ever many rebuilds you wish to do, rebuild once and, unless the backbone looks badly angled in which case ignore it, shake.
3) Take the best result from 2) and do a wiggle/shake
4) If the resulting score is reasonably close to the score of the starting structure, do some limited fuzing and hope for an improvement

Dialog settings

Rebuild length: The size of segments to be rebuilt. 5, 6, or 7 are probably your best bets.

Number of rebuilds: How many rebuild/shake attempts to make.

Min residue/Max residue: The defaults are 1 and the number of residues in the protein respectively, but changing these lets you focus on a particular region.

Loops only: If unchecked, it'll pay no attention to the secondary structure. If checked, it'll rebuild sections that are loops only and sections containing a single non-loop residue.

Joined: 04/15/2012
Groups: Beta Folders
Not Bad

I like it. It boosted my score by 150 in less than half an hour. Good job!

tim1079's picture
User offline. Last seen 3 years 29 weeks ago. Offline
Joined: 07/21/2010
Groups: None
This program gets stuck on

This program gets stuck on the detect secondary structure function call.


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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, Boehringer Ingelheim, RosettaCommons