The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
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DOI：
10.1038/nature06684
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发表时间：
2008-03-06
期刊：
影响因子：
64.8
通讯作者：
Major, Francois
中科院分区：
文献类型：
--
作者：
Parisien, Marc;Major, Francois
经典的RNA二级结构模型考虑了A.U和G.U沃森-克里克以及G.U摆动碱基对。在这里，我们用一个新的取代它，其中一组核苷酸环基序定义RNA结构。该模型允许我们在一个有效的评分函数中统一所有碱基配对的能量贡献，以解决RNA折叠问题。我们展示了基于核苷酸循环基序MC- Fold和MC- Sym的流水线两种计算机算法如何从序列中再现一系列实验确定的RNA三维结构。这证明了考虑所有碱基配对相互作用在填补序列和结构之间的空白方面是多么重要。我们使用该管道来定义前体microRNA以双螺旋折叠的规则，尽管存在许多假定的错配和凸起，并提出了人类免疫缺陷病毒的新模型- 1-1移框元件。
The classical RNA secondary structure model considers A.U and G.U Watson - Crick as well as G.U wobble base pairs. Here we substitute it for a new one, in which sets of nucleotide cyclic motifs define RNA structures. This model allows us to unify all base pairing energetic contributions in an effective scoring function to tackle the problem of RNA folding. We show how pipelining two computer algorithms based on nucleotide cyclic motifs, MC- Fold and MC- Sym, reproduces a series of experimentally determined RNA three- dimensional structures from the sequence. This demonstrates how crucial the consideration of all base- pairing interactions is in filling the gap between sequence and structure. We use the pipeline to define rules of precursor microRNA folding in double helices, despite the presence of a number of presumed mismatches and bulges, and to propose a new model of the human immunodeficiency virus- 1-1 frame- shifting element.