Tools To Model Rna Structure?

Question

[Payal]

Dear Friends,

Could anyone suggest to me any tool (not any online tools) like modeller9.9 (for proteins) to model a nucleic acid structure?

Thanks in advance..

[Pierre Lindenbaum]

Related: http://biostar.stackexchange.com/questions/8909/dna-secondary-structure-prediction-of-a-large-dataset

Answer 1

[Larry_Parnell]

What most people use is the Vienna RNA Package for RNA Secondary Structure Prediction and Comparison

A list of what is available:

RNAfold -- predict minimum energy secondary structures and pair probabilities
RNAeval -- evaluate energy of RNA secondary structures
RNAheat -- calculate the specific heat (melting curve) of an RNA sequence
RNAinverse -- inverse fold (design) sequences with predefined structure
RNAdistance -- compare secondary structures
RNApdist -- compare base pair probabilities
RNAsubopt -- complete suboptimal folding
RNAplot -- RNA structure drawings in PostScript, SVG, or GML
RNAcofold -- predict hybrid structure of two sequences
RNAduplex -- predict possible hybridization sites between two sequences
RNAup -- predict RNA-RNA interaction sites using accessibilities
RNAalifold -- predict the consensus structure of several aligned sequences
RNAaliduplex -- comparative (multiple alignment) version of RNAduplex
RNALfold -- predict locally stable structure of long sequences
RNAplfold -- compute average pair probabilities for local base pairs in long sequences
RNApaln -- fast structural alignment of RNA sequences using string alignments
Several small but helpful Perl Utilities

I am sure that you will have a few other options from other respondents.

[Darren J. Fitzpatrick]

I recommend this one. I did a project using it a few years back and it is fairly straightforward to implement. You can test some of the functionality using the web service - http://rna.tbi.univie.ac.at/

[Larry_Parnell]

I agree, Darren. We use it to assess allele-specific differences in folding of 3'-UTRs.

Answer 2

[Asaf]

For a 3D model (and also for 2D) you can try Assemble: http://www.ncbi.nlm.nih.gov/pubmed/20562414

Answer 3

[Michael]

Did you try Locomotif for designing 2D-structures?