Department of Mathematics, University of California, Berkeley, 94720, USA.
Bull Math Biol. 2011 Apr;73(4):754-76. doi: 10.1007/s11538-010-9607-3. Epub 2011 Jan 5.
Motivated by recent work in parametric sequence alignment, we study the parameter space for scoring RNA folds and construct an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common branching. We use this polytope and its normal fan to study the effect of varying three parameters in the free energy model that are not determined experimentally. Our results indicate that variation of these specific parameters does not have a dramatic effect on the structures predicted by the free energy model. We additionally map a collection of known RNA secondary structures to the RNA polytope.
受最近参数序列比对工作的启发，我们研究了 RNA 折叠的参数空间，并构建了一个 RNA 多面体。该多面体的一个顶点对应于具有常见分支的 RNA 二级结构。我们使用这个多面体及其法向扇区来研究在自由能模型中三个未经验证的参数的变化的影响。我们的结果表明，这些特定参数的变化对自由能模型预测的结构没有显著影响。我们还将一组已知的 RNA 二级结构映射到 RNA 多面体上。
