We have used DOT to dock DNA to proteins but increasingly need to examine computational models for RNA docking onto proteins. Would appreciate advice and examples where this has proven successful.
I have used HADDOCK (http://www.bonvinlab.org/software/haddock2.2/) - information-driven felxible docking approach for modelling protein-protein, protein-nucleic acid and protein-ligand complexes. The results include additional scripts for further analysis and scoring, which is very helpful.