Prediction of RNA base pairings yields insight into molecular structure, and therefore function. The most common methods predict an optimal structure under the standard thermodynamic model. One component of this model is the equation which governs the cost of branching, where three or more helical "arms" radiate out from a multiloop (also known as a junction). The multiloop initiation equation has three parameters; changing those values can significantly alter the predicted structure. We give a complete analysis of the prediction accuracy, stability, and robustness for all possible parameter combinations for a diverse set of tRNA sequences, and also for 5S rRNA. We find that the accuracy can often be substantially improved on a per sequence basis. However, simultaneous improvement within families, and most especially between families, remains a challenge.

中文翻译：

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RNA分支预测的挑战：热力学优化下多环起始的参数分析。

RNA碱基配对的预测可深入了解分子结构，从而发挥作用。最常见的方法是在标准热力学模型下预测最佳结构。该模型的一个组成部分是控制分支成本的方程式，其中三个或更多的螺旋“臂”从多回路（也称为接合点）辐射出来。多回路启动方程具有三个参数：更改这些值会大大改变预测的结构。我们对各种tRNA序列以及5S rRNA的所有可能参数组合给出了预测准确性，稳定性和鲁棒性的完整分析。我们发现，通常可以在每个序列的基础上显着提高准确性。但是，家庭内部，尤其是家庭之间的同时改善，