The challenge of RNA branching prediction: a parametric analysis of multiloop initiation under thermodynamic optimization
The challenge of RNA branching prediction: a parametric analysis of multiloop initiation under thermodynamic optimization
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DOI：
10.1016/j.jsb.2020.107475
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发表时间：
2020-04-01
影响因子：
3
通讯作者：
Heitsch, Christine
中科院分区：
文献类型：
--
作者：
Poznanovic, Svetlana;Barrera-Cruz, Fidel;Heitsch, Christine
RNA碱基配对的预测有助于深入了解分子结构，从而了解功能。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，其中三个或更多个螺旋“臂”从多环（也称为结）辐射出来。多回路引发方程有三个参数;改变这些值可以显着改变预测的结构。我们对各种rRNA序列以及5S rRNA序列的所有可能参数组合的预测准确性、稳定性和稳健性进行了完整的分析。我们发现，准确性往往可以大大提高每个序列的基础上。然而，家庭内部，特别是家庭之间的同时改善仍然是一个挑战。
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 rRNA 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.