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Recipe: HNetwork Probe 2.0
Created by spvincent 36 15
Your rating: None Average: 4.3 (14 votes)


Name: HNetwork Probe 2.0
ID: 103779
Created on: Thu, 08/06/2020 - 07:46
Updated on: Thu, 08/06/2020 - 14:46

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spvincent's picture
User offline. Last seen 11 hours 14 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Joined: 09/24/2012
Groups: Go Science
Great explanation

Thanks for the method explained in the Wiki. And for the recipe of course.

LociOiling's picture
User offline. Last seen 4 hours 14 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
a little more info...

Here are a few things I've found out about how HNetwork Probe works.

The recipe has two ways to specify which segments to mutate:

  1. If "select unfrozen" is checked, only segments with unfrozen sidechains are mutated.
  2. Otherwise, the "mutate segments" box can be used to specify numeric ranges of segments, such as "1-3,6,19-30,45-62". The recipe will try to mutate the segments in these ranges, as long as they are mutable and have unfrozen sidechains.

You must use one or the other of these methods.

The "amino acids" box lists the amino acids the recipe will try when mutating.

The recipe disables all filters except "Hydrogen Bond Network". (Call it HBN for short.) The recipe mainly checks the HBN score, and not the overall score.

The recipe initially mutates each specified segment to a random amino acid from the list specified in the dialog. The recipe then does a minimal wiggle sidechains. This is the start of a "run".

The recipe then picks one mutable from the ones specified, and tries up to five further mutations on it. The recipe does a minimal wiggle sidechains after each mutation.

If the HBN score improves, the new pose is saved in a quick save slot, and a message is printed. Otherwise, the recipe just keeps going, again making random mutations to each specified segment, starting another "run".

Each run includes the random mutate of all the specified segments, plus a new random pick of the segment to focus on for five more mutations.

The recipe is quiet unless there's a gain, so the output window may not change for a long time.

The recipe only does wiggle sidechains, there's no shake sidechains or wiggle backbone.

The recipe stops when the specified range of quick save slots it exhausted. In many cases, this means the recipe runs until you cancel it.

The recipe turns off undo processing at the start. At the end, it turns undo processing back on, and then loads each quick save slot it used, in sequence. In theory, this means you should see the best hydrogen bond network score when the recipe terminates. Undo or control-z gets you the next best HBN score, and so on.

The recipe is focused on the best hydrogen bond network score. If there's a gain, you should see the pose with the best HBN score at the end. If there's no gain, the protein will just be left where it was when you cancelled the recipe. You'll need to restore credit best or load a previous save.

The recipe does not re-enable any conditions at the end, so the final score will almost certainly be invalid, unless you're working on a test puzzle which includes only an HBN condition.

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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