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Recipe: Local Quake 4.0
Created by spvincent 41 23
Your rating: None Average: 4.6 (94 votes)


Name: Local Quake 4.0
ID: 45320
Created on: Mon, 02/04/2013 - 13:07
Updated on: Mon, 02/04/2013 - 21:07

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spvincent's picture
User offline. Last seen 6 hours 43 min ago. Offline
Joined: 12/07/2007
Groups: Contenders

Changes since 3.1:

1) Algorithmic improvements and speed up
2) Option added to ensure bands to a helix are also reasonably perpendicular to that helix, in an attempt to avoid the common problem with banding scripts of helix mangling,
3) Dialog control over many other parameters.

Algorithm outline:

1) Pick an amino acid (call it a node)

2) Create bands from that node to its nearest neighbours (see comments in script for how this is done)

3) Wiggle

4) Delete bands and wiggle sidechains (used to be a shake in previous versions but wiggle seems to work just as well and is a lot faster)

5) Wiggle and hope for an improvement from the starting score

Doesn't do any fuzing and generally tries to optimize for speed.

Notes on dialog settings:

Min/Max residue: Nodes will only be created within this region of the protein but bands radiating from this node may extend anywhere.

Target reduction: The band strength is set so that after creating the bands, wiggle will occur until the score drops by approximately this amount. Supreme precision is not attempted here: the script readjusts band strength based on whether the wiggle in the previous quake overshot or undershot this value although large errors are corrected on the fly.

Max bands: The maximum number of bands allowable from each node.

Min/Max band length: To aid in controlling/localizing the effects of the Quake.

N nodes: the number of nodes to be created.

Distance between nodes: If more than one node will be this far apart along the protein. A value of 0 is allowed and will result in a single centre. The default value of 3 seems to work well: because the number of residues in a helix turn is 3.6 this means that in the case of a helix both quake centres will be on approximately the same side and less likely to mangle it: a bit of a general problem with Quake-style scripts.

Change after: After this number of quakes without any improvement in the score, change the distance between nodes to something random. Default 10.
Inverse scale: If true (default), then inversely scale the band strength with length: in other words long bands will be weaker. The idea is to help localize the effects of the quake.

Disallow helix || bands: (||= parallel : there's not enough room to spell it out in the dialog box). When checked, bands that are bound to a helix at either end will only be allowed if they are reasonably perpendicular to the helix: reasonably being defined in terms of a specified angle (kMaxAllowableAngle) Small helices (4 residues or less) are unaffected. It doesn't tend to matter if such helices become distorted and the angle calculation becomes even more inexact anyway.

Mutate not shake: This checkbox will appear if and only if the puzzle contains mutable residues. If set, the side chain wiggle in the algorithm will be replaced by a mutate. Not sure how useful this is.

Joined: 02/10/2013
Groups: Gargleblasters
Great script!

This has helped on several puzzles. I find a shake after a bit helps immensely.

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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