[Dock-fans] RNA-Ligand Docking with DOCK6

Christian Schudoma schudoma at mpimp-golm.mpg.de
Mon Feb 18 00:45:39 PST 2008

Thanks Scott,
> 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?


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