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Recipe: Stack's Starter
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Name: Stack's Starter
ID: 49234
Created on: Wed, 05/28/2014 - 20:39
Updated on: Sun, 06/08/2014 - 06:25
Description:

Automatically assign secondary structures for a new fold solution



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Joined: 03/18/2014
Groups: Gargleblasters
Stack's Starter

What it's for:
An opening script for design or prediction puzzles. It assigns secondary structures to the fold for you.

How to use:
The manual option is good for design puzzles, you can for example, tell it to setup 4 helices. It will calculate and assign for you so that they're all the same size and distance.

The automatic option can be useful for prediction puzzles. It estimates some likely structures in the fold. I have come up with this feature from reading blogs and articles - this is handy if the puzzle is freestyle or has only 1 starting position. It is never spot on but often gives a good rough guide.

Joined: 09/24/2012
Groups: Go Science
suggestion

Thanks !

Suggestion:

-allow selecting a zone (from seg - to seg)

With this option, one could run the recipe one time for the first helixes, then another time for successive sheets etc.
It would also be useful if we only want to set a new structure for a bad zone of an existing protein.

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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