Allow limit of possible AAs in mutate function

Case number:845813-992379
Topic:Game: Tools
Opened by:Rav3n_pl
Status:Open
Type:Suggestion
Opened on:Saturday, April 14, 2012 - 00:13
Last modified:Friday, April 20, 2012 - 22:26

In some situations we want to limit changes when mutating. Adding table of usable aas to mutate function as optional parameter would be useful sometimes.
Like we have TNT puzzles long time ago - some of chains was "desired". In ligand puzzles when we move ligand too close mutate always make glycyne - we not want this sometimes.

[written under brow42 suggestion]

(Sat, 04/14/2012 - 00:13  |  7 comments)


Joined: 05/03/2009
Groups: Contenders

I'm very very curious why you would decide to limit your explore options Brow42? And also define your 'discard' options?

....and actually how you have decided how to define that 'margin of error'?

I'm just curious :)

CFC

Joined: 06/17/2010

In some cases I just not want to make gly or pro (ie when it is part of sheet/helix).
I have no control on mutate function.

Joined: 05/03/2009
Groups: Contenders

Maybe it's a Scripter v Non-Scripter point of view :)

Joined: 06/17/2010

Tru! :D

brow42's picture
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Mainly, it started out with frustration at the mutate sidechains/mutate combo/mutate all turning everything into Pro or Gly if I moved the ligand too close, and I'd have to undo or mutate by hand to get polar sidechains back, plus I'd lost 20 minutes to brute force mutate just to get 2 gly and a pro.

Lately, I've been thinking about a mutate function that was configurable...pass in any combination of: all hydrophobe (except pro, gly), all hydrophilic, MALEK, , pro, and gly, or a custom list.

As for the TNT puzzles...before my time.

Obviously, this can all be done in pure Lua, but I suppose the C implementation might do something smarter, like pick-random-until-improvement or something, and be significantly faster at that.

infjamc's picture
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You're not the only one-- I mentioned a similar issue 3 years ago: http://fold.it/portal/node/986508

brow42's picture
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I just wanted to perma-cross-link this feedback here: http://fold.it/portal/node/992394 as another example. I think the docking puzzles have stimulated a lot of new ideas. That feedback notes a preference for aromatic sidechains at many interfaces.

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