| class="wikitable sortable"
! Name
! Description | Institution | Links | References |
| European Nucleotide Archive
|Secondary structure prediction based on generalized centroid estimator | no | [http://www.ncrna.org/centroidfold/ sourcecode] [http://www.ncrna.org/centroidfold/ webserver] | [{{cite journal | author = Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai | title = Predictions of RNA secondary structure using generalized centroid estimators | journal = Bioinformatics | volume = 25 | issue = 4 | pages = 465–473 | year = 2009 | pmid = 16873527 | doi = 10.1093/bioinformatics/btn601 }}] |
| GenBank
|Secondary 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. | no | [http://contra.stanford.edu/contrafold/ sourcecode] [http://contra.stanford.edu/contrafold/server.html webserver] | [{{cite journal | author = Do CB, Woods DA, Batzoglou S | title = CONTRAfold: RNA secondary structure prediction without physics-based models | journal = Bioinformatics | volume = 22 | issue = 14 | pages = e90–8 | year = 2006 | pmid = 16873527 | doi = 10.1093/bioinformatics/btl246 }}] |
| DNA Data Bank of Japan
|Secondary structure prediction method based on placement of helices allowing complex pseudoknots. | yes | [http://cylofold.abcc.ncifcrf.gov/ webserver] | [{{cite journal | author = Bindewald E, Kluth T, Shapiro BA | title = CyloFold: secondary structure prediction including pseudoknots | journal = Nucleic Acids Research | volume = Suppl | issue = W | pages = 368-72 | year = 2010 | pmid = 20501603 | doi = 10.1093/nar/gkq432 }}] |
| KineFold
|Folding kinetics of RNA sequences including pseudoknots by including an implementation of the partition function for knots. | yes | [http://kinefold.curie.fr/ linuxbinary,] [http://kinefold.curie.fr/cgi-bin/form.pl webserver] | [{{cite journal | author = Xayaphoummine A, Bucher T, Isambert H | title = Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots | journal = Nucleic Acids Res. | volume = 33 | issue = Web Server issue | pages = W605–10 | year = 2005 | pmid = 15980546 | doi = 10.1093/nar/gki447 | pmc = 1160208 }}][{{cite journal | author = Xayaphoummine A, Bucher T, Thalmann F, Isambert H | title = Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 100 | issue = 26 | pages = 15310–5 | year = 2003 | pmid = 14676318 | doi = 10.1073/pnas.2536430100 | pmc = 307563 }}] |
| Mfold
|MFE RNA structure prediction algorithm. | no | [http://www.bioinfo.rpi.edu/applications/mfold/ sourcecode,] [http://frontend.bioinfo.rpi.edu/applications/hybrid/quikfold.php webserver] | [{{cite journal | author = Zuker M, Stiegler P | title = Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information | journal = Nucleic Acids Res. | volume = 9 | issue = 1 | pages = 133–48 | year = 1981 | pmid = 6163133 | doi = 10.1093/nar/9.1.133 | pmc = 326673 }}] |
| Pknots
|A dynamic programming algorithm for optimal RNA pseudoknot prediction using the nearest neighbour energy model. | yes | [http://selab.janelia.org/software.html sourcecode] | [{{cite journal | author = Rivas E, Eddy SR | title = A dynamic programming algorithm for RNA structure prediction including pseudoknots | journal = J. Mol. Biol. | volume = 285 | issue = 5 | pages = 2053–68 | year = 1999 | pmid = 9925784 | doi = 10.1006/jmbi.1998.2436 }}] |
| PknotsRG
|A dynamic programming algorithm for the prediction of a restricted class of RNA pseudoknots. | yes | [http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/welcome.html sourcecode,] [http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/submission.html webserver] | [{{cite journal | author = Reeder J, Steffen P, Giegerich R | title = pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows | journal = Nucleic Acids Res. | volume = 35 | issue = Web Server issue | pages = W320–4 | year = 2007 | pmid = 17478505 | doi = 10.1093/nar/gkm258 | pmc = 1933184 }}]
| |
| RNAfold
|MFE RNA structure prediction algorithm. Includes an implementation of the partition function for computing basepair probabilities and circular RNA folding. | no | [http://www.tbi.univie.ac.at/~ivo/RNA/ sourcecode,] [http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi webserver] | [{{cite journal | author = I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster | title = Fast Folding and Comparison of RNA Secondary Structures. | journal = Monatshefte f. Chemie | volume = 125 | pages = 167–188 | year = 1994 | doi = 10.1007/BF00818163}}][{{cite journal | author = McCaskill JS | title = The equilibrium partition function and base pair binding probabilities for RNA secondary structure | journal = Biopolymers | volume = 29 | issue = 6-7 | pages = 1105–19 | year = 1990 | pmid = 1695107 | doi = 10.1002/bip.360290621 }}][{{cite journal | author = Hofacker IL, Stadler PF | title = Memory efficient folding algorithms for circular RNA secondary structures | journal = Bioinformatics | volume = 22 | issue = 10 | pages = 1172–6 | year = 2006 | pmid = 16452114 | doi = 10.1093/bioinformatics/btl023 }}][{{cite journal | author = Bompfünewerer AF, Backofen R, Bernhart SH, et al. | title = Variations on RNA folding and alignment: lessons from Benasque | journal = J Math Biol | volume = 56 | issue = 1-2 | pages = 129–144 | year = 2008 | pmid = 17611759 | doi = 10.1007/s00285-007-0107-5 }}][{{cite book|title=The Hitchhiker's Guide to the Galaxy|author=Douglas Adams|published=1979|isbn=0-330-25864-8|year=1979|publisher=Pan Books|location=London}}] |
| RNAshapes
|MFE 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. | no | [http://bibiserv.techfak.uni-bielefeld.de/download/tools/rnashapes.html source & binaries,] [http://bibiserv.techfak.uni-bielefeld.de/rnashapes/ webserver] | [{{cite journal | author = R. Giegerich, B.Voß, M. Rehmsmeier | title = Abstract shapes of RNA. | journal = Nucleic Acids Res. | volume = 32 | issue = 16 | pages = 4843–4851 | year = 2004 | doi = 10.1093/nar/gkh779 | pmid = 15371549 | pmc = 519098}}][{{cite journal | author = B. Voß, R. Giegerich, M. Rehmsmeier | title = Complete probabilistic analysis of RNA shapes. | journal = BMC Biology | volume = 4 | issue = 5 | year = 2006 | doi = 10.1186/1741-7007-4-5 | pmid = 16480488 | pages = 5 | pmc = 1479382}}] |
| RNAstructure
|A program to predict lowest free energy structures and base pair probabilities for RNA or DNA sequences. Structure prediction can be constrained using experimental data, including SHAPE, enzymatic cleavage, and chemical modification accessibility. Graphical user interfaces are available for Windows and for Mac OS-X/Linux. Programs are also available for use with Unix-style text interfaces. Additionally, a C++ class library is available. | no | [http://rna.urmc.rochester.edu/RNAstructure.html source & binaries] | [{{cite journal | doi = 10.1073/pnas.0401799101 | author = D.H. Mathews, M.D. Disney, J. L. Childs, S.J. Schroeder, M. Zuker, D.H. Turner | title = Incorporating chemical modification constraints into a dynamic programming algorothm for prediction of RNA secondary structure. | journal = Proceedings of the National Academy of Sciences, USA | volume = 101 | issue = 19 | pages = 7287–7292 | year = 2004 | pmid = 15123812 | pmc = 409911 }}][{{cite journal | author = D.H. Mathews | title = Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. | journal = RNA | volume = 10 | pages = 1178–1190 | year = 2004 | pmid = 15272118 | issue = 8 | doi = 10.1261/rna.7650904 | pmc = 1370608 }}] |
| Sfold
|Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities. | no | [http://sfold.wadsworth.org/srna.pl webserver] | [{{cite journal | author = Ding Y, Lawrence CE | title = A statistical sampling algorithm for RNA secondary structure prediction | journal = Nucleic Acids Res. | volume = 31 | issue = 24 | pages = 7280–301 | year = 2003 | pmid = 14654704 | doi = 10.1093/nar/gkg938 | pmc = 297010 }}][{{cite journal | author = Ding Y, Chan CY, Lawrence CE | title = Sfold web server for statistical folding and rational design of nucleic acids | journal = Nucleic Acids Res. | volume = 32 | issue = Web Server issue | pages = W135–41 | year = 2004 | pmid = 15215366 | doi = 10.1093/nar/gkh449 | pmc = 441587 }}][{{cite journal | author = Ding Y, Chan CY, Lawrence CE | title = RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble | journal = RNA | volume = 11 | issue = 8 | pages = 1157–66 | year = 2005 | pmid = 16043502 | doi = 10.1261/rna.2500605 | pmc = 1370799 }}][{{cite journal | author = Chan CY, Lawrence CE, Ding Y | title = Structure clustering features on the Sfold Web server | journal = Bioinformatics | volume = 21 | issue = 20 | pages = 3926–8 | year = 2005 | pmid = 16109749 | doi = 10.1093/bioinformatics/bti632 }}] |
| UNAFold
|The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. | no | [http://www.bioinfo.rpi.edu/applications/hybrid/download.php sourcecode] | [{{cite journal |author=Markham NR, Zuker M |title=UNAFold: software for nucleic acid folding and hybridization. |journal=Methods Mol Biol |volume=453 |issue= |pages=3–31 |year=2008 |pmid=18712296 |doi=10.1007/978-1-60327-429-6_1}}] |
| colspan="7" | *Knots: Pseudoknot prediction, . |