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Recipe: HNetwork Probe 1.0
Created by spvincent 32 26
4.57143
Your rating: None Average: 4.6 (7 votes)

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Name: HNetwork Probe 1.0
ID: 102977
Created on: Mon, 12/31/2018 - 18:34
Updated on: Tue, 01/01/2019 - 02:34
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spvincent's picture
User offline. Last seen 1 hour 7 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
This is a script that's

This is a script that's intended to help with creating Hydrogen Bond Networks. It's something of a blunt instrument but the resultant poses can help serve as a starting point for future work.

The idea is to make a limited selection of residues in an area where networks might plausibly form, randomly mutate them to amino acids that have either hydrogen bond donors or acceptors, wiggle the sidechains, and then, if any hydrogen bond networks form, store them in quicksave slots.

Selecting the residues to mutate.

Two ways this can be done: select unfrozen residues only or explicitly list the residues to mutate. Because of the fairly inefficient nature of this script, it's desirable to limit this number: I've found 20 or so to be a reasonable maximum but your mileage may vary. If you have existing networks; you can freeze them and use either of the methods below, but I occasionally see the script throw up false positives under these circumstances.

Select unfrozen

If checked, use the first option described above. For the purposes of this script it doesn't matter if the backbone or side chain is frozen.

Mutate segments

Relevant iff Select unfrozen above is not selected (I find this the more useful way of doing things). List the residues to mutate (ranges are allowed) separated by commas in a way already used by many other scripts; e.g. 34,36,41-44, etc.

Amino acids

The list of possible replacements. All amino acids that contain a donor or acceptor are included; however it might be wise to prune this list a bit depending on circumstances: for example if you are looking for networks in the core of the complex you might want to omit lysine (k) and arginine (r). While you may well get more networks the hiding and sidechain score penalties will likely to be too great to make them worthwhile.

Filter threshold

Of questionable utility: this can probably be ignored. Only gains in the HNet filter greater than this value will be recorded.

The script chugs away: any networks found will be saved in quicksave slots (13+) and a suitable message printed out in the Recipe Output window. It's recommended that you kill the script when you've got a few networks and take a look (enable all the filters; show networks; freeze the residues that make up the network; mutate and wiggle)

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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