[Dock-fans] RNA-Ligand Docking with DOCK6

Scott Brozell sbrozell at scripps.edu
Thu Feb 14 23:44:38 PST 2008


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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