A novel knowledge-based potential for RNA 3D structure evaluation
A novel knowledge-based potential for RNA 3D structure evaluation
复制标题
RNA 3D 结构评估的新的基于知识的潜力
DOI：
10.1088/1674-1056/27/3/038701
复制
发表时间：
2018-03-01
影响因子：
1.7
通讯作者：
Shao，Zhi-Gang
中科院分区：
文献类型：
--
作者：
Yang，Yi;Gu，Qi;Shao，Zhi-Gang
核糖核酸（RNA）在生物学中起着至关重要的作用，并且需要了解其三维（3D）结构以了解其生物学功能。近年来，人们提出了一些结构预测方法来解决这一问题，但大多数现有的方法通常只能预测一系列RNA的三维结构。因此，对预测结构的评价通常是必不可少的。虽然已经提出了几种方法来评估RNA的3D结构，但现有的方法不够精确。在这项工作中，一个新的全原子知识为基础的潜力，更准确地评估RNA的三维结构。该势函数不仅包括局部和非局部相互作用，而且通过引入再训练机制，充分考虑了每个RNA的特异性。基于从独立的方法产生的广泛的测试集，所提出的潜在的正确区分的天然状态和排名近天然构象，以有效地选择最好的。此外，所提出的潜在精确捕获RNA的结构特征，如碱基堆积和碱基配对。与现有的潜在方法的比较表明，所提出的潜力是非常可靠和准确的RNA三维结构评估。
Ribonucleic acids (RNAs) play a vital role in biology, and knowledge of their three-dimensional (3D) structure is required to understand their biological functions. Recently structural prediction methods have been developed to address this issue, but a series of RNA 3D structures are generally predicted by most existing methods. Therefore, the evaluation of the predicted structures is generally indispensable. Although several methods have been proposed to assess RNA 3D structures, the existing methods are not precise enough. In this work, a new all-atom knowledge-based potential is developed for more accurately evaluating RNA 3D structures. The potential not only includes local and nonlocal interactions but also fully considers the specificity of each RNA by introducing a retraining mechanism. Based on extensive test sets generated from independent methods, the proposed potential correctly distinguished the native state and ranked near-native conformations to effectively select the best. Furthermore, the proposed potential precisely captured RNA structural features such as base-stacking and base-pairing. Comparisons with existing potential methods show that the proposed potential is very reliable and accurate in RNA 3D structure evaluation.