The algorithms central to RNAstructure are based on the following sources. Research benefitting from these capabilities encapsulated within RNAstructure should cite the appropriate sources.
Most current folding parameters:
D.H. Mathews, M.D. Disney, J.L. Childs, S.J. Schroeder, M. Zuker, and D.H. Turner.
"Incorporating Chemical Modification Constraints into a Dynamic Programming Algorithm for Prediction of RNA Secondary Structure."
Proceedings of the National Academy of Sciences USA, 101:7287-7292. (2004).
Previous reference to the folding algorithm, with details on thermodynamic parameter derivation:
D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner.
"Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure."
Journal of Molecular Biology, 288:911-940. (1999).
Prediction of secondary structures at temperatures other than 37°C:
Z.J. Lu, D.H. Turner, and D.H. Mathews.
"A Set of Nearest Neighbor Parameters for Predicting the Enthalpy Change of RNA Secondary Structure Formation."
Nucleic Acids Research, 34(17):4912-24. (2006).
Partition function for calculating base pair probabilities:
D.H. Mathews.
"Using an RNA Secondary Structure Partition Function to Determine Confidence in Base Pairs Predicted by Free Energy Minimization."
RNA, 10:1178-1190. (2004).
Dynalign:
D.H. Mathews.
"Predicting a Set of Minimal Free Energy Secondary Structures Common to Two Sequences."
Bioinformatics, 21:2246-2253. (2005).
Extensive use of Dynalign (for extensive acceleration of the algorithm):
A. Harmanci, G. Sharna, and D.H. Mathews.
"Efficient Pairwise RNA Structure Prediction Using Probabilistic Alignment Constraints in Dynalign."
BMC Bioinformatics, 8:130-150. (2007).
Previous reference to Dynalign:
D.H. Mathews and D.H. Turner.
"Dynalign: An Algorithm for Finding the Secondary Structure Common to Two RNA Sequences."
Journal of Molecular Biology, 317:191-203. (2002).
OligoScreen:
O.V. Mateeva, D.H. Mathews, A.D. Tsodikov, S.A. Shabalina, R.F. Gesteland, J.F. Atkins, and S.M. Freier.
"Thermodynamic Criteria for High Hit Rate Antisense Oligonucleotide Design."
Nucleic Acids Research, 31:4989-4994. (2003).
OligoWalk:
D.H. Mathews, M.E. Burkard, S.M. Freier, J.R. Wyatt, and D.H. Turner.
"Predicting Oligonucleotide Affinity to Nucleic Acid Targets."
RNA, 5:1458-1469. (1999).
DNA/RNA duplex parameters for DNA oligomers:
N. Sugimoto, S. Nakano, A. Katoh, H. Nakamura, T. Ohmichi, M. Yoneyama, and M. Sasaki.
"Thermodynamic Parameters to Predict the Stability of RNA/DNA Hybrid Duplexes."
Biochemistry, 34:11211-11216. (1995).
Prediction of all suboptimal secondary structures:
S. Dian, D.H. Mathews, and D.H. Turner.
"Interpreting Oligonucleotide Microarray Data to Determine RNA Secondary Structure. Application to the 3' End of Bombyx mori R2 DNA."
Biochemistry, 45:9819-9832. (2006).
Methods for predicting suboptimal secondary structures:
D.H. Mathews.
"Revolutions in RNA Secondary Structure Prediction."
Journal of Molecular Biology, 359:526-532. (2006).
Original reference to generating all suboptimal secondary structures for a sequence:
S. Wuchty, W. Fontant, I,L. Hofacker, and P. Schuster.
"Complete Suboptimal Folding of RNA and the Stability of Secondary Structures."
Biopolymers, 49:145-165. (1999).
Stochastic sampling:
Y. Ding and C.E. Lawrence.
"A Statistical Sampling Algorithm for RNA Secondary Structure Prediction."
Nucleic Acids Research, 31:7280-7301. (2003).
Using SHAPE data to constrain structure prediction:
K.E. Deigan, T.W. Li, D.H. Mathews, and K.M. Weeks.
"Accurate SHAPE-directed RNA Structure Determination."
Proceedings of the National Academy of Sciences USA, 106: 97-102. (2009).
Photocleavage of uracil in the presence of FMN:
P. Burgstaller, T. Hermann, C. Huber, E. Westhof, and M. Famulok.
"Isoalloxazine derivatives promote photocleavage of natural RNAs at G.U base pairs embedded within helices."
Nucleic Acids Ressearch, 25:4018-4027. (1997).
ProbKnot pseudoknot prediction algorithm:
S. Bellaousov and D. H. Mathews.
"ProbKnot: fast prediction of RNA secondary structure including pseudoknots."
RNA, 16:1870-1880. (2010).
Multilign:
Z. Xu and D. H. Mathews.
"Multilign: An algorithm to predict secondary structures conserved in multiple RNA sequences."
Bioinformatics, 27:626-632. (2011)
TurboFold:
A. O. Harmanci, H. Sharma,and D. H. Mathews
"TurboFold: Iterative Probabilistic Estimation of Secondary Structures for Multiple RNA Sequences."
BMC Bioinformatics, 12:108. (2011).
