[Dock-fans] RNA-Ligand Docking with DOCK6

[Scott Brozell]

Hi,

On Fri, 15 Feb 2008, Francesco Pietra wrote:

> 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.

Possibly, some memory related improvements have been made.

Scott

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