Another idea on sidechain mutation

Case number:845813-986508
Topic:Game: Tools
Opened by:infjamc
Status:Open
Type:Suggestion
Opened on:Thursday, July 16, 2009 - 13:07
Last modified:Thursday, July 19, 2012 - 19:38

Currently, the "mutate sidechains" command is known to be slow. Since there may be situations where one does not need to consider all 20 amino acids for a position, it would be useful if there is an option to manually define a set of residues to pick at each location (so that the process of automatic mutation could be sped up). For example:

* All 20 amino acids (default)
* Don't mutate at this location (useful if the user still wants to consider a shake for the position)
* All except cysteine (if unexpected disulfides is an issue)
* Hydrophobics only
* Aromatics only
* Hydrophilics only
* Charged only
* Positively-charged only
* Negatively-charged only
* Custom (the user defines the residues to pick)

(Thu, 07/16/2009 - 13:07  |  4 comments)


Joined: 12/14/2008

There is a ticket with "mutate only one sidechain", meaning the selected.

However, this can be modified as "only selected" sidechains. And freezing would prevent mutate (don't know if it is now).

* All except cysteine (if unexpected disulfides is an issue)
* Hydrophobics only
* Aromatics only
* Hydrophilics only
* Charged only
* Positively-charged only
* Negatively-charged only

I think only the difference between hydrophobics and philies is useful here, and more options overkill. That is something that no normal players knows about. At least not in details that would be needed for a real decision.

infjamc's picture
User offline. Last seen 2 years 45 weeks ago. Offline
Joined: 02/20/2009
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As much I hate to resurrect an old thread, this feature could be useful for Puzzles like 271: Hold It 2. In this case, a possible application might be limiting the set of amino acids to "All except for Arg/Lys/Asp/Glu," so that the -1000 side chain penalty doesn't come up in a design that actually does fulfill the conditions...

Joined: 06/17/2010

Bump.
It can be done in script (mutate one by one, skipping that we not want) but limited auto mutate would be nice.

brow42's picture
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Joined: 09/19/2011
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Circularly linking http://fold.it/portal/node/992379 from here, more discussion on the subject.

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