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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