Free energy minimization, secondary structure prediction

Mathews, D. H., and Turner, D. H. (2006). Prediction of RNA secondary structure by free energy minimization. Cun. Opin. Struct. Biol. 16, 270-278. 

Doshi, K., Cannone, J., Cobaugh, C., and Gutell, R. (2004) Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics 5, 105. 

This preliminary report presents recent progress in secondary structure prediction based on free energy minimization. The following changes have been implemented The method for forcing base pairs has been improved. A filter that removes isolated Watson-Crick or G-U base pairs (those that cannot stack on any other Watson-Crick or G-U pair) has been incorporated. Recently measured free energies for 2 by 2 internal loops (Xia, T. McDowell, J. A. Turner, D. H. In preparation.), 2 by 1 internal loops (75), and hairpin loops 18) have also been incorporated. Finally, a new model for coaxial stacking of helixes has been developed. 

An algorithm based upon a dynamic programing concept has been described by Jernigan et al. for minimizing the free energy of a polypeptide, and utilized for secondary structure prediction. In a study with the aid of UNICEPP of the binding of flexible substrate molecules within the cleft region of lysozyme (EC... 

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