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. Name Description KnotsKnots: Pseudoknot prediction, <yes|no>. Links References CentroidFoldSecondary structure prediction based on generalized centroid estimator sourcecode webserver CentroidHomfoldSecondary structure prediction by using homologous sequence information sourcecode webserver Context FoldAn RNA secondary structure prediction software based on feature-rich trained scoring models. sourcecode webserver CONTRAfoldSecondary structure prediction method based on conditional log-linear models (CLLMs), a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. sourcecode webserverCrumpleSoftware that produces a full set of possible secondary structures for a given sequence, using optional constraints. sourcecode CyloFoldSecondary structure prediction method based on placement of helices allowing complex pseudoknots. webserver E2EfoldA deep learning based method for efficiently predicting secondary structure by differentiating through a constrained optimization solver, without using dynamic programming. sourcecodeChen, X., Li, Y., Umarov, R., Gao, X., and Song, L. RNAsecondary structure prediction by learning unrolled algorithms. In International Conference on Learning Representations, 2020. URL https://openreview.net/forum?id=S1eALyrYDH.EternaFoldA multitask-learning-based model trained on data from the Eterna project. sourcecode webserver GTFold Fast and scalable multicore code for predicting RNA secondary structure. link sourcecodeINTERPINAlgorithm and database for prediction of transcription termination sites in bacteria. Uses Mfold for RNA secondary structure prediction.webserver IPknotFast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. sourcecode webserver KineFoldFolding kinetics of RNA sequences including pseudoknots by including an implementation of the partition function for knots. linuxbinary, webserver MfoldMFE (Minimum Free Energy) RNA structure prediction algorithm. sourcecode, webserver pKissA dynamic programming algorithm for the prediction of a restricted class (H-type and kissing hairpins) of RNA pseudoknots. , webserver PknotsA dynamic programming algorithm for optimal RNA pseudoknot prediction using the nearest neighbour energy model. sourcecode PknotsRGA dynamic programming algorithm for the prediction of a restricted class (H-type) of RNA pseudoknots. sourcecode, webserver RNA123Secondary structure prediction via thermodynamic-based folding algorithms and novel structure-based sequence alignment specific for RNA. webserver SQUARNASecondary structure prediction via stem maximization sourcecode webserver RNAfold MFE RNA structure prediction algorithm. Includes an implementation of the partition function for computing basepair probabilities and circular RNA folding. sourcecode, webserver RNAshapesMFE RNA structure prediction based on abstract shapes. Shape abstraction retains adjacency and nesting of structural features, but disregards helix lengths, thus reduces the number of suboptimal solutions without losing significant information. Furthermore, shapes represent classes of structures for which probabilities based on Boltzmann-weighted energies can be computed. source & binaries, webserver RNAstructureA program to predict lowest free energy structures and base pair probabilities for RNA or DNA sequences. Programs are also available to predict maximum expected accuracy structures and these can include pseudoknots. Structure prediction can be constrained using experimental data, including SHAPE, enzymatic cleavage, and chemical modification accessibility. Graphical user interfaces are available for Windows, Mac OS X, Linux. Programs are also available for use with Unix-style text interfaces. Also, a C++ class library is available. source & binaries, webserver SARNA-PredictRNA Secondary structure prediction method based on simulated annealing. It can also predict structure with pseudoknots. link seqfoldPredict the minimum free energy structure of nucleic acids. seqfold is an implementation of the Zuker, 1981 dynamic programming algorithm, the basis for UNAFold/mfold, with energy functions from SantaLucia, 2004 (DNA) and Turner, 2009 (RNA). MIT license. Python CLI or module. link & sourceSfoldStatistical sampling of all possible structures. The sampling is weighted by partition function probabilities. Github_RepositorySliding Windows & AssemblySliding windows and assembly is a tool chain for folding long series of similar hairpins. sourcecode SPOT-RNASPOT-RNA is first RNA secondary structure predictor which can predict all kind base pairs (canonical, noncanonical, pseudoknots, and base triplets). sourcecode webserverSwiSpotCommand-line utility for predicting alternative (secondary) configurations of riboswitches. It is based on the prediction of the so-called switching sequence, to subsequently constrain the folding of the two functional structures. sourcecodeUFoldUFold: fast and accurate RNA secondary structure prediction with deep learning sourcecode, webserver UNAFoldCommand-line utility for predicting alternative (secondary) configurations of riboswitches. It is based on the prediction of the so-called switching sequence, to subsequently constrain the folding of the two functional structures. sourcecode vsfold/vs suboptFolds and predicts RNA secondary structure and pseudoknots using an entropy model derived from polymer physics. The program vs_subopt computes suboptimal structures based on the free energy landscape derived from vsfold5. webserverNotes
Single sequence tertiary structure prediction Name Description KnotsKnots: Pseudoknot prediction, <yes|no>. Links References trRosettaRNAtrRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions by trRosettaRNA are competitive to the predictions by the top human groups on natural RNAs. webserver sourcecode BARNACLEA Python library for the probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA-like on a local length scale. sourcecode FARFAR2Automated de novo prediction of native-like RNA tertiary structures . webserver iFoldRNAthree-dimensional RNA structure prediction and folding webserver MC-Fold MC-Sym Pipeline Thermodynamics and Nucleotide cyclic motifs for RNA structure prediction algorithm. 2D and 3D structures. sourcecode, webserver NASTCoarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters executables NuFold A deep learning-based tertiary structure prediction method built upon AlphaFold 2 architecture. Utilizes flexible nucleobase center representation and metagenomic multiple sequence alignment to further predictions. executables MMBTurning limited experimental information into 3D models of RNA sourcecode RNA123Integrated platform for de novo and homology modeling of RNA 3D structures, where coordinate file input, sequence editing, sequence alignment, structure prediction and analysis features are all accessed from one intuitive graphical user interface. RNAComposerFully automated prediction of large RNA 3D structures. webserver webserver Notes
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.