AN RNA FOLDING METHOD CAPABLE OF IDENTIFYING PSEUDOKNOTS AND BASE TRIPLES

Motivation: Recently, we described a Maximum Weighted Matching (MWM) m ethod for RNA structure prediction. The MWM method is capable of detec ting pseudoknots and other tertiary base-pairing interactions in a com putationally efficient manner (Cary and Stormo, Proceedings of the Thi rd International Conference on Intelligent Systems for Molecular Biolo gy pp. 75-80, 1995). Here we report on the results of our efforts to i mprove the MWM method's predictive accuracy and show how the method ca n be extended to detect base interactions formerly inaccessible to aut omated RNA modeling techniques. Results: Improved performance in MWM s tructure prediction was achieved in two ways. First, new ways of calcu lating base pair likelihoods have been developed. These allow experime ntal data and combined statistical and thermodynamic information to be used by the program. Second, accuracy was improved by developing tech niques for filtering out spurious base pairs predicted by the MWM prog ram. We also demonstrate here a means by which the MWM folding method may be used to detect the presence of base triples in RNAs.