[Dock-fans] RNA-Ligand Docking with DOCK6

Scott Brozell sbrozell at scripps.edu
Mon Feb 18 23:51:04 PST 2008


Hi,

On Mon, 18 Feb 2008, Christian Schudoma wrote:

> > 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.
> So, the preferred scoring function for RNA-ligand docking would be Amber 
> scoring with DOCK 6.2? Or have the other scoring functions available in 
> the current version already been modified to suit the physical 
> properties of RNA? By the way, do I have to reapply for a DOCK license 
> to obtain 6.2?

All the scoring functions should be ok.
I am not aware of any scoring function being substantially better
than any other.  An old license should be ok.

Scott





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