Dear Please use http://its2.bioapps.biozentrum.uni-wuerzburg.de/

This is the best interface i found till for RNA modeling

There are several methods for homology modeling of RNA. I suggest you to start with ModeRNA. It is simple in use and has a webserver: (http://iimcb.genesilico.pl/modernaserver/). It allows you not only to create homology models but also to clean structure, check geometry or select best template for modeling.

Also RNABuilder is a tool devoted for homology modeling. Well documented and easy to use but no possibility to select template as far as I am concerned.

hi:

if you are using more than one template ''MOE'' will be the best tool in my opinion

Homology modeling of RNA is typically not done or if it is done it is not done well. Aside from Amber dynamic simulations, you could try RNA123 from DNASoft (http://www.rna123.com/). This program was specifically designed for RNA homology modeling and includes an energy minimization step. It has a 30 day free trial if you want to test it.

I think for you the EMBL resource centre will be very helpfull, they have good nucleotide sequences of both DNA & RNA, just check the attached link

http://www.ebi.ac.uk/ena/

thank you all for ur valuable answers. am very new to this subject. may b am silly pls just clarify me, as Krzysztof wicher said modelling of secondary structure. and how its differs from homology modelling (in accuracy). bcoz i used rna composer to get 3d model from secondary structure and i also want a validation tool for the model, like savs for protein