I find so many limitations in working with nucleic acid structures. pardon me, if I am wrong. When I try to model some 500 nucleotides nucleic acid structure(mRNA), I don't find any good tools like protein homology modeling tools for nucleic acid structure. Similarly I don't find any tools for RNA-RNA docking.
Seeing all these constraints, now my doubt is "Is prediction of nucleic acid structure and their docking studies (miRNA-mRNA) meaningful?
Could anyone suggest me some RNA-RNA docking tools? which is more valid? Please attach some reference too.
The reason RNA structure prediction is so behind protein structure is because the structure of RNA is much more complex than that of proteins. AFAIK modeling of RNA-RNA interactions is made based on the secondary structure only.
There are several tools that can predict RNA interactions, among them RNAup, intaRNA, RNAhybrid and more. Their predictive value is not high (this is an understatement) for miRNA and sRNA targets.
Indeed RNA folding/simulation is not on par with that of proteins... Nevertheless, if you are confident of your mRNA structures, some programs do support RNA (see HADDOCK) and allow docking between two of these molecules. If you are not confident of your models however, there's not much you can do..
Regarding modelling RNA, I would recommend MC-sym / MC-fold (modelling) and modeRNA (homology modelling).
Thanks @asaf for your valuable suggestion...