Coarse-grained RNA folding models promise great potential for RNA structure prediction. A key component in a coarse-grained folding model is the force field. One of the challenges in the coarse-grained force field calculation is how to treat the correlation between the different degrees of freedoms. Here, we describe a new approach (IsRNA) to extract the correlated energy functions from the known structures. Through iterative molecular dynamics simulations, we build the correlation effects into the reference states, from which we extract the energy functions. The validity of IsRNA is supported by the close agreement between the simulated Boltzmann-like probability distributions for all the structure parameters and those observed from the experimentally determined structures. The correlated energy functions derived here may provide a new tool for RNA 3D structure prediction.

中文翻译：

---

IsRNA：建模RNA折叠中的相关相互作用的迭代模拟参考状态方法。

粗粒RNA折叠模型有望为RNA结构预测提供巨大潜力。粗粒度折叠模型中的关键要素是力场。粗粒度力场计算中的挑战之一是如何处理不同自由度之间的相关性。在这里，我们描述了一种从已知结构中提取相关能量功能的新方法（IsRNA）。通过迭代分子动力学模拟，我们将相关效应建立到参考状态中，从中提取能量函数。对于所有结构参数的模拟玻尔兹曼样概率分布与从实验确定的结构观察到的概率分布之间的紧密一致性，支持了IsRNA的有效性。