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Recipe: SimpleRebuilder_0.2
Created by lilovip 79 1445
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Name: SimpleRebuilder_0.2
ID: 2250
Created on: Fri, 03/12/2010 - 12:55
Updated on: Fri, 03/12/2010 - 20:55
Description:

Powerful tool for automatic rebuilding. Finds and rebuilds loop sequence (all segments between helices and sheets), then shakes, wiggles and restores recent best. Does this few times depending on loop score and length (highly configurable) for every loop sequence and many times for whole protein. There are lots of optimizations: doesn't process repeated poses, doesn't useless wiggles and shakes etc. Actually, this is script "Run it and go to bad". You can divide long loops by some single helix segments and script will recognize them as separators. Also you can change the last segments of helices and sheets to loops temporaly for script working to increase loop flexibility. There are many parameters to change at the begin of scripts.



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lilovip's picture
User offline. Last seen 1 year 26 weeks ago. Offline
Joined: 11/11/2009
Groups: None
Important

As you can see, there are many improvements of the version 0.1. Now it's really powerful and fast tool. Usually, it gives me 300-500 points at middle game with 2-8 hours processing.
I need some help with this script configuring. I need your advices for parameters values. Especially I need more accurate values for: repeatLoopMinByScore, repeatLoopMaxByScore, repeatLoopMinByLength, repeatLoopMaxByLength and very especially for loopScoreImportance value. If you have any considerations for these parameters correcting, please let me know here!
Also, I want to ask: which loops should be rebuilt with more priority: loops with lesser average score or loops with lesser minimal score of segments ("problem segments")? Now first variant is realised.
I'm planing to add algorithm for automatic division of very long loops. Do you have any suggestions how that algorithm should behave?
If you like this tool, please, vote for SimpleRebuilder_0.1 too. Thanks.

lilovip's picture
User offline. Last seen 1 year 26 weeks ago. Offline
Joined: 11/11/2009
Groups: None
Error here!

Don't try to download this script. This one was uploaded when server was full. I haven't ANY backup of this script, so whole-night work is lost. I will rewrite this script later.

To admins: please try to backup this script! If not, delete this 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