Waldispühl Jérôme, Reinharz Vladimir
School of Computer Science, McGill University, 3480 University Street, Room 318, Montreal, QC, Canada, H3A 0E9,
Methods Mol Biol. 2015;1269:101-21. doi: 10.1007/978-1-4939-2291-8_6.
Modeling the three-dimensional structure of RNAs is a milestone toward better understanding and prediction of nucleic acids molecular functions. Physics-based approaches and molecular dynamics simulations are not tractable on large molecules with all-atom models. To address this issue, coarse-grained models of RNA three-dimensional structures have been developed. In this chapter, we describe a graphical modeling based on the Leontis-Westhof extended base-pair classification. This representation of RNA structures enables us to identify highly conserved structural motifs with complex nucleotide interactions in structure databases. Further, we show how to take advantage of this knowledge to quickly and simply predict three-dimensional structures of large RNA molecules.
对RNA的三维结构进行建模是更好地理解和预测核酸分子功能的一个里程碑。基于物理学的方法和分子动力学模拟对于具有全原子模型的大分子来说是难以处理的。为了解决这个问题，已经开发了RNA三维结构的粗粒度模型。在本章中，我们描述了一种基于Leontis-Westhof扩展碱基对分类的图形建模方法。这种RNA结构表示使我们能够在结构数据库中识别具有复杂核苷酸相互作用的高度保守的结构基序。此外，我们展示了如何利用这些知识快速、简单地预测大型RNA分子的三维结构。
