[Dock-fans] RNA-Ligand Docking with DOCK6

Francesco Pietra chiendarret at yahoo.com
Fri Feb 15 09:57:49 PST 2008


Hi Scott:
In order to plan my work, may I ask if Dock6.2 has reduced the memory use of
Orient::match_ligand? If the answer is already implied in your last few mails,
I beg pardon.
Cheers
francesco pietra

--- Scott Brozell <sbrozell at scripps.edu> wrote:

> Hi,
> 
> On Wed, 13 Feb 2008, Christian Schudoma wrote:
> 
> > I am a PhD student in structural bioinformatics, trying to use DOCK6 for 
> > docking ligands into RNA molecules, in particular riboswitches. Are the 
> > DOCK6 scoring functions suitable for this task, i.e. have NA-specific 
> > parameters been integrated into the latest DOCK version? In the 
> > dockfans-archives I found a brief statement (Feb 2005) that comparison 
>
http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2005-February/000038.html
> > of "a variety of charge models for RNA" have been under way. Have these 
> > comparisons been fruitful? I wasn't able to find further or even 
> > concluding information about this even after intensive research.
> >
> > If such modifications have not been made yet, does anyone have 
> > experience with successfully docking to RNA targets and is willing to 
> > share their parameters/scoring settings? Any help would be appreciated!
> > (I already know about the article by Kang et al. (2003) =) )
> 
> The test set used for "DOCK 6", which will be available after 6.2
> is released, is an RNA suite.  And it includes some riboswitches.
> As far as RNA's, 6.1 is essentially the same as 6.2 except for Amber score.
> There will be some new scripts to handle RNAs for Amber score. 
> (In 6.1 and 6.0 the amberize scripts assume that an NA is a DNA.)
> 6.2 will be released very soon.
> 
> Scott
> 
> 
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> 



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