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Recipe: Local Mutate 1.0 (NC)
Created by spvincent 24 17
Your rating: None Average: 4.4 (32 votes)


Name: Local Mutate 1.0 (NC)
ID: 48061
Created on: Tue, 02/04/2014 - 21:01
Updated on: Wed, 02/05/2014 - 05:01

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spvincent's picture
User offline. Last seen 1 hour 36 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
A script similar in style to

A script similar in style to Rav Mutate. For design puzzles and optimized for NC.

Algorithm outline

For each amino acid
Set the Clash Importance to something low
Select everything in the immediate neighbourhood of that residue
Shake at low CI
Set the CI to 1 and select the whole protein
Wiggle sidechains
Record any improvement

Dialog settings

Min residue, Max residue

The range to be mutated : by default the whole protein. The script will go through this range twice with offset start points processing alternate residues each time: each individual residue is processed only once.

Target loss

An approximation only: controlled by varying the CI during the initial mutate. In practise, depending whether the loss exceeds or falls short of the target, the CI will be increased or reduced for the next residue processed: not the current one. Mutate is slow and supreme accuracy is not required here: additionally the set of amino acids mutated for each residue is unlikely to vary too greatly.

Mutate radius

Every amino acid within this distance of the one currently being processed will be mutated. Reduce to make the script run faster.

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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