Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France.
Cold Spring Harb Perspect Biol. 2011 Feb 1;3(2):a003632. doi: 10.1101/cshperspect.a003632.
A general approach for modeling the architecture of large and structured RNA molecules is described. The method exploits the modularity and the hierarchical folding of RNA architecture that is viewed as the assembly of preformed double-stranded helices defined by Watson-Crick base pairs and RNA modules maintained by non-Watson-Crick base pairs. Despite the extensive molecular neutrality observed in RNA structures, specificity in RNA folding is achieved through global constraints like lengths of helices, coaxiality of helical stacks, and structures adopted at the junctions of helices. The Assemble integrated suite of computer tools allows for sequence and structure analysis as well as interactive modeling by homology or ab initio assembly with possibilities for fitting within electronic density maps. The local key role of non-Watson-Crick pairs guides RNA architecture formation and offers metrics for assessing the accuracy of three-dimensional models in a more useful way than usual root mean square deviation (RMSD) values.
描述了一种用于对大型结构 RNA 分子结构建模的通用方法。该方法利用了 RNA 结构的模块化和层次折叠特性，将其视为由沃森-克里克碱基对定义的预形成双链螺旋和由非沃森-克里克碱基对维持的 RNA 模块的组装。尽管在 RNA 结构中观察到广泛的分子中性，但 RNA 折叠的特异性是通过全局约束来实现的，例如螺旋的长度、螺旋堆积的共轴性以及螺旋连接点采用的结构。Assemble 集成了计算机工具套件，可用于序列和结构分析，以及通过同源建模或从头组装进行交互式建模，并具有在电子密度图中拟合的可能性。非沃森-克里克碱基对的局部关键作用指导 RNA 结构的形成，并提供了评估三维模型准确性的指标，比通常的均方根偏差 (RMSD) 值更有用。
