Abstract
Prediction of RNA structure from nucleotide sequence remains an unsolved grand challenge of biochemistry and requires distinct concepts from protein structure prediction. We report a stepwise Monte Carlo method that has enabled the first blind prediction recovering all noncanonical base pairs of a complex RNA structure, a double pseudoknot from the Zika virus genome posed as a community-wide RNA Puzzle. A benchmark of 82 diverse motif structure challenges and prospective experimental tests for three previously unsolved tetraloop/receptors support the method’s general ability to recover noncanonical pairs ab initio, with remaining problems traced to limitations of current macromolecule free energy functions.
Copyright
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