Why you need DNA/RNA structure prediction. You can download crystal structures from www.pdb.org

u cn try HADDOCK server (http://haddock.chem.uu.nl/dna/dna.php)

try Assemble for RNA 3D structure prediction

hi,

try out RNA123 with this link

http://www.rna123.com/

Hi

I think you use gromacs software that calculate simulation DNA & protein.

For RNA: FARNA (basically Rosetta for RNA), MC-Sym/MC-Fold, iFoldRNA, NAST/C2S, MANIP/Assemble (should be part of a pipeline called Paradise), ModeRNA (homology modeling)

For DNA: A one-sided coin should do the trick... (Yes, I know about DNA that diverges from the typical helical structure, but as far as I know there's no prediction method for that available). If you really have to model a helix: use the make-na server.

@Gopi Mohan: Yea, you can download structures from the PDB/NDB. But what if your target RNA is not covered by those databases? It's the same as in the protein world... "why prediction? -> because there's no known structure".

@Nutan Chauhan: Cool, I had no idea about that tool.

u can simply use discovery or Schrodinger software available on computational info

Dear Muhammad sulaman nawaz,

you may refer this paper

@Abdul Razak Mohamed Sikkander: There's not one single mention of RNA 3D structure prediction in your pasted article...Neither of DNA 3D...what exactly is the point of this?

A more appropriate reading on "current" RNA 3D prediction would be Shapiro et al (2007) Bridging the gap in RNA structure prediction. http://www.ncbi.nlm.nih.gov/pubmed/17383172

This is an active area of research and not as fully developed as protein prediction.

Good software furthermore needs to be defined, and possibly judged on the accuracy of the prediction , perhaps based on family type of RNA/DNA, and usability/efficiency of the software.

Below are couple of additional links that are attempting such a comparison.

________________

http://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software

http://openwetware.org/wiki/Wikiomics:RNA_secondary_structure_prediction

Hi Muhammad ! Try Visual Molecular Dynamics (Linux open source i think) at Beckman Institute.

Hope i helped !

Kindest regards to you !

Zoltan

I have used PatchDock and HADdock. Those were fine.

This link

http://bioinfo3d.cs.tau.ac.il/PatchDock/

hi try "CLC Main Workbench 6" or "CLC Sequence Viewer 6"

Anyone know software for protein-DNA docking?

I am surprised that no one mentioned Rosetta. Rosetta (www.rosettacommons.org)has been used to design binding proteins for DNA and has RNA ab initio folding.

I suggest you look at the publications from the Das lab: http://www.stanford.edu/~rhiju/

This lab is also responsible for EteRNA, a game modeled after fold.it. Pretty cool stuff: http://eterna.cmu.edu/eterna_page.php?page=me_tab

Like Chandrajit Bajaj said, this area of research is fairly new. There really are no straight answers.

@Steven Combs: The Rosetta method for RNA is called FARNA (with FARFAR extension) and I listed it in one of the earlier answers, even mentioning that it's "basically Rosetta for RNA". Checking the whole thread and searching for keywords sometimes helps to avoid being surprised ;D

You may find some important software packages in OSDDlinux, try http://osddlinux.osdd.net/

You can use NUCGEN at http://nucleix.mbu.iisc.ernet.in/nucgen2/ for building DNA and RNA duplexes. FIbre model s well sequence dependent models.

MD in implicit water model.

For example with Abalone http://www.biomolecular-modeling.com/Abalone/index.html

you can use mfold server for both DNA and RNA

This is the list for Protein, DNA, RNA, Glycan modeling.

http://www.vls3d.com/index.php/links/bioinformatics/3d-structure-prediction/protein-dna-rna-glycan-modeling