[Dock-fans] RNA-Ligand Docking with DOCK6

Christian Schudoma schudoma at mpimp-golm.mpg.de
Wed Feb 13 03:33:08 PST 2008

Hello everyone,

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 
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) =) )

Thanks and regards,

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