Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

@article{Mathews1999ExpandedSD,
  title={Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.},
  author={David H. Mathews and Jeffrey Sabina and Michael Zuker and Douglas H. Turner},
  journal={Journal of molecular biology},
  year={1999},
  volume={288 5},
  pages={
          911-40
        }
}
An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization. Thermodynamic parameters for the stabilities of secondary structure motifs are revised to include expanded sequence dependence as revealed by recent experiments. Additional algorithmic improvements include reduced search time and storage for multibranch loop free energies and improved imposition of folding constraints. An extended database of 151,503 nt in 955 structures… 

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References

SHOWING 1-10 OF 104 REFERENCES

Improved predictions of secondary structures for RNA.

The accuracy of computer predictions of RNA secondary structure from sequence data and free energy parameters has been increased to roughly 70% and the excellent performance is consistent with these interactions being the primary interactions determiningRNA secondary structure.

An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints.

A new procedure which allows for the incorporation of constraints before and during the process of RNA folding is described and SAPSSARN is an interactive program which offers a framework, both to specify a secondary structure through a set of folding constraints and to compute all the supoptimal saturated RNA secondary structures which satisfy all the folding constraints.

Improved parameters for the prediction of RNA hairpin stability.

The nearest neighbor model allows prediction of RNA hairpin stability to within 5-10% of the experimentally measured values and provides good agreement with the measured values for both T(M) ( within 10 degrees C of the measured value) and deltaGo(37) (within 0.8 kcal/mol of the measurement value).

Improved free-energy parameters for predictions of RNA duplex stability.

  • S. FreierR. Kierzek D. Turner
  • Biology, Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 1986
These parameters predict melting temperatures of most oligonucleotide duplexes within 5 degrees C, about as good as can be expected from the nearest-neighbor model.

Thermodynamic prediction of conserved secondary structure: application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein.

The algorithm combines the advantages of thermodynamic structure prediction by energy minimization with the information obtained from phylogenetic alignment of sequences to give a consensus probability matrix emphasizing the conserved secondary structure elements of the RNA set.

On finding all suboptimal foldings of an RNA molecule.

The mathematical problem of determining how well defined a minimum energy folding is can now be solved and all predicted base pairs that can participate in suboptimal structures may be displayed and analyzed graphically.

The equilibrium partition function and base pair binding probabilities for RNA secondary structure

A novel application of dynamic programming to the folding problem for RNA enables one to calculate the full equilibrium partition function for secondary structure and the probabilities of various substructures by a recursive scheme of polynomial order N3 in the sequence length N.

Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin.

Analysis of the thermodynamics of folding of combinatorial libraries is general and may be applied to a wide variety of complex nucleic acid secondary and tertiary motifs in order to identify the stable and unstable members.

An APL-programmed genetic algorithm for the prediction of RNA secondary structure.

The possibilities of using a genetic algorithm for the prediction of RNA secondary structure were investigated, and a fair number of correct stems are predicted, even when using computationally quick, but very crude, fitness criteria such as stem length and stacking energy.

A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides.

The results allow the development of a model to predict the stability of RNA hairpin loops and the model gives good agreement when tested against four naturally occurring hairpin sequences.
...