This list of RNA structure prediction software is a compilation of software tools and web portals used for nucleic acid structure prediction.
Single sequence secondary structure prediction.
Single sequence tertiary structure prediction
Comparative methods The single sequence methods mentioned above have a difficult job detecting a small sample of reasonable secondary structures from a large space of possible structures. A good way to reduce the size of the space is to use evolutionary approaches. Structures that have been conserved by evolution are far more likely to be the functional form. The methods below use this approach.
RNA solvent accessibility prediction
Intermolecular interactions: RNA-RNA Many ncRNAs function by binding to other RNAs. For example, miRNAs regulate protein coding gene expression by binding to 3' UTRs, small nucleolar RNAs guide post-transcriptional modifications by binding to rRNA, U4 spliceosomal RNA and U6 spliceosomal RNA bind to each other forming part of the spliceosome and many small bacterial RNAs regulate gene expression by antisense interactions E.g. GcvB, OxyS and RyhB.
Intermolecular interactions: MicroRNA:any RNA The below table includes interactions that are not limited to UTRs.
Intermolecular interactions: MicroRNA:UTR MicroRNAs regulate protein coding gene expression by binding to 3' UTRs, there are tools specifically designed for predicting these interactions. For an evaluation of target prediction methods on high-throughput experimental data see (Baek et al., Nature 2008), (Alexiou et al., Bioinformatics 2009), or (Ritchie et al., Nature Methods 2009)
ncRNA gene prediction software
Family specific gene prediction software
RNA homology search software
Benchmarks
Alignment viewers, editors
Inverse folding, RNA design
Notes
Secondary structure viewers, editors
See also RNA Non-coding RNA RNA structure Comparison of nucleic acid simulation software Comparison of software for molecular mechanics modeling
References