2 title={Optimal computer folding of large {RNA} sequences using thermodynamics and auxiliary information},
3 author={Zuker, M. and Stiegler, P.},
4 journal={Nucleic acids research},
9 publisher={Oxford Univ Press}
11 @article{mccaskill:1990,
12 title={The equilibrium partition function and base pair binding probabilities for {RNA} secondary structure},
13 author={McCaskill, J.S.},
14 journal={Biopolymers},
19 publisher={Wiley Online Library}
22 @article{mathews:2004,
23 title={Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of {RNA} secondary structure},
24 author={Mathews, D.H. and Disney, M.D. and Childs, J.L. and Schroeder, S.J. and Zuker, M. and Turner, D.H.},
25 journal={Proceedings of the National Academy of Sciences of the United States of America},
30 publisher={National Acad Sciences}
33 @article{mathews:1999,
34 title={Expanded sequence dependence of thermodynamic parameters improves prediction of {RNA} secondary structure},
35 author={Mathews, D.H. and Sabina, J. and Zuker, M. and Turner, D.H. and others},
36 journal={Journal of molecular biology},
41 publisher={Elsevier Science}
44 @article{turner:2010 ,
45 title={{NNDB}: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure},
46 author={Turner, D.H. and Mathews, D.H.},
47 journal={Nucleic Acids Research},
52 publisher={Oxford Univ Press}
56 title={{RNA} structure prediction},
57 author={Turner, D.H. and Sugimoto, N. and Freier, S.M.},
58 journal={Annual review of biophysics and biophysical chemistry},
63 publisher={Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}
67 title={Improved predictions of secondary structures for {RNA}},
68 author={Jaeger, J.A. and Turner, D.H. and Zuker, M.},
69 journal={Proceedings of the National Academy of Sciences},
74 publisher={National Acad Sciences}
77 title={Nearest-neighbor parameters for {G-U} mismatches: {5'GU3'}/{3'UG5'} is destabilizing in the contexts {CGUG/GUGC}, {UGUA/AUGU}, and {AGUU/UUGA} but stabilizing in {GGUC/CUGG}},
78 author={He, L. and Kierzek, R. and SantaLucia Jr, J. and Walter, A.E. and Turner, D.H.},
79 journal={Biochemistry},
84 publisher={ACS Publications}
87 title={Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops},
88 author={Peritz, A.E. and Kierzek, R. and Sugimoto, N. and Turner, D.H.},
89 journal={Biochemistry},
94 publisher={ACS Publications}
97 title={Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of {RNA} folding},
98 author={Walter, A.E. and Turner, D.H. and Kim, J. and Lyttle, M.H. and M{\"u}ller, P. and Mathews, D.H. and Zuker, M.},
99 journal={Proceedings of the National Academy of Sciences},
104 publisher={National Acad Sciences}
106 @article{bruccoleri:1988,
107 title={An improved algorithm for nucleic acid secondary structure display},
108 author={Bruccoleri, R.E. and Heinrich, G.},
109 journal={Computer applications in the biosciences: CABIOS},
114 publisher={Oxford Univ Press}
116 @article{hofacker:1994a,
117 title={The rules of the evolutionary game for {RNA}: {A} statistical characterization of the sequence to structure mapping in {RNA}},
118 author={Hofacker, I.L. and Organisiert, C.F.},
123 title = {{T}he {H}itchhikers {Guide} to the {G}alaxy},
124 author = {Douglas Adams},
128 @article{dimitrov:2004,
129 title={Prediction of hybridization and melting for double-stranded nucleic acids},
130 author={Dimitrov, R.A. and Zuker, M.},
131 journal={Biophysical Journal},
139 @article{hofacker:1994,
140 title={Fast folding and comparison of {RNA} secondary structures},
141 author={Hofacker, I.L. and Fontana, W. and Stadler, P.F. and Bonhoeffer, L.S. and Tacker, M. and Schuster, P.},
142 journal={Monatshefte f{\"u}r Chemie/Chemical Monthly},
150 @article{hofacker:2002,
151 title={Secondary structure prediction for aligned {RNA} sequences},
152 author={Hofacker, I.L. and Fekete, M. and Stadler, P.F.},
153 journal={Journal of molecular biology},
160 @article{hofacker:2006,
161 title={Memory efficient folding algorithms for circular {RNA} secondary structures},
162 author={Hofacker, I.L. and Stadler, P.F.},
163 journal={Bioinformatics},
168 publisher={Oxford Univ Press}
170 @article{bernhart:2008,
171 title={{RNAalifold}: Improved consensus structure prediction for {RNA} alignments},
172 author={Bernhart, S.H. and Hofacker, I.L. and Will, S. and Gruber, A.R. and Stadler, P.F.},
173 journal={BMC bioinformatics},
178 publisher={BioMed Central Ltd}
180 @article{bernhart:2006,
181 title={Partition function and base pairing probabilities of {RNA} heterodimers},
182 author={Bernhart, S.H. and Tafer, H. and M{\"u}ckstein, U. and Flamm, C. and Stadler, P.F. and Hofacker, I.L.},
183 journal={Algorithms for Molecular Biology},
188 publisher={BioMed Central Ltd}
190 @article{fontana:1993a,
191 title={Statistics of {RNA} secondary structures},
192 author={Fontana, W. and Konings, D.A.M. and Stadler, P.F. and Schuster, P.},
193 journal={Biopolymers},
198 publisher={Wiley Online Library}
200 @article{fontana:1993b,
201 title={{RNA} folding and combinatory landscapes},
202 author={Fontana, W. and Stadler, P.F. and Bornberg-Bauer, E.G. and Griesmacher, T. and Hofacker, I.L. and Tacker, M. and Tarazona, P. and Weinberger, E.D. and Schuster, P.},
203 journal={Physical review E},
210 @article{shapiro:1990,
211 title={Comparing multiple {RNA} secondary structures using tree comparisons},
212 author={Shapiro, B.A. and Zhang, K.},
213 journal={Computer applications in the biosciences: CABIOS},
218 publisher={Oxford Univ Press}
220 @article{shapiro:1988,
221 title={An algorithm for comparing multiple {RNA} secondary structures},
222 author={Shapiro, B.A.},
223 journal={Computer applications in the biosciences: CABIOS},
228 publisher={Oxford Univ Press}
231 @article{lorenz:2012,
232 title = {{RNA} Folding Algorithms with {G-Quadruplexes}},
233 author = {Lorenz, Ronny and Bernhart, Stephan H. and Externbrink, Fabian and Qin, Jing and H{\"{o}}ner zu Siederdissen, Christian and Amman, Fabian and Hofacker, Ivo L. and Stadler, Peter F.},
236 abstract = {G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes. Using a simple but plausible energy model for quadruplexes, we find that the overwhelming majority of putative quadruplex-forming sequences in the human genome are likely to fold into canonical secondary structures instead.}
239 @article{lorenz:2011,
240 title={{ViennaRNA} Package 2.0},
241 author={Lorenz, Ronny and Bernhart, Stephan H. and H{\"o}ner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L.},
242 journal={Algorithms for Molecular Biology},
247 publisher={BioMed Central Ltd},
248 doi={10.1186/1748-7188-6-26},
249 abstract={BACKGROUND: Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties.\\
250 RESULTS: The ViennaRNA Package has been a widely used compilation of RNA secondary structure related computer programs for nearly two decades. Major changes in the structure of the standard energy model, the Turner 2004 parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic variants prompted a major technical overhaul of both the underlying RNAlib and the interactive user programs. New features include an expanded repertoire of tools to assess RNA-RNA interactions and restricted ensembles of structures, additional output information such as centroid structures and maximum expected accuracy structures derived from base pairing probabilities, or z-scores for locally stable secondary structures, and support for input in fasta format. Updates were implemented without compromising the computational efficiency of the core algorithms and ensuring compatibility with earlier versions.\\
251 CONCLUSIONS: The ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be downloaded from www.tbi.univie.ac.at/RNA }
254 @InProceedings{lorenz:2009,
255 editor = {Grosse, Ivo and Neumann, Steffen and Posch, Stefan
256 and Schreiber, Falk and Stadler, Peter F.},
257 author = {Lorenz, Ronny and Flamm, Christoph and Hofacker, Ivo L.},
258 title = {2D Projections of {RNA} folding Landscapes},
259 booktitle = {German Conference on Bioinformatics 2009},
264 isbn = {978-3-88579-251-2},
265 publisher = {Gesellschaft f.\ Informatik},
267 series = {Lecture Notes in Informatics},
268 abstract = {The analysis of RNA folding landscapes yields insights into the kinetic folding
269 behavior not available from classical structure prediction methods. This is especially
270 important for multi-stable RNAs whose function is related to structural changes,
271 as in the case of riboswitches. However, exact methods such as barrier tree analysis
272 scale exponentially with sequence length. Here we present an algorithm that computes
273 a projection of the energy landscape into two dimensions, namely the distances
274 to two reference structures. This yields an abstraction of the high-dimensional energy
275 landscape that can be conveniently visualized, and can serve as the basis for estimating
276 energy barriers and refolding pathways. With an asymptotic time complexity of O(n^7)
277 the algorithm is computationally demanding. However, by exploiting the sparsity of
278 the dynamic programming matrices and parallelization for multi-core processors, our
279 implementation is practical for sequences of up to 400 nt, which includes most RNAs
280 of biological interest.}