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Recipe: Mutate No Wiggle 2.2
Created by LociOiling 4 2
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Name: Mutate No Wiggle 2.2
ID: 102570
Created on: Thu, 12/07/2017 - 13:39
Updated on: Thu, 12/07/2017 - 21:39
Description:

Brute Force Mutator, but doesn't wiggle, stabilize, or fuze. Keeps best AA for each spot. Good for slow design puzzles. Has options for restricting mutations. Version 1.2 lets you exclude alanine. Version 1.3 works on locked segments and lets you repeat a specified number of times. Version 1.4 shuffles the order of segments after the first round. The first round is in segment score order. Version 1.5 sets an adjustable minimum gain threshold to avoid wasting time on miniscule gains. Version 1.6 offers a "polars only" option and streamlines reporting. V 1.7 adds tyrosine ('Y') to the polar list. Version 2.0 revamps the pause function. Version 2.1 adds enforcement of recent design puzzle rules and improves printing of options. Version 2.2 has a special ligand mode.



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LociOiling's picture
User offline. Last seen 5 hours 23 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
ligand mode

For ligand puzzles, there a new "Ligand" button in the bottom row. It lets you specify a sphere size. Only segments within the specified distance of the ligand are mutated.

As with the existing "Select" dialog, after the "Ligand" dialog, the segments to be processed are shown as ranges in the "Where" field of the main dialog. The list of segments may get cut off due to the fixed size of "Where", but you can copy and paste to see the full list.

This version of the recipe use structure.GetDistance to measure the distances. It doesn't attempt to find the nearest atoms of the segment and the ligand.

This version also assumes that the interesting ligand is the very last segment. We had a recent puzzle where this was not the case, with an interesting small molecule ligand followed by three boring single-atom ligands. This recipe will need updating if that situation arises again.

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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