Automated 3D structure composition for large RNAs.
Automated 3D structure composition for large RNAs.
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DOI：
10.1093/nar/gks339
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发表时间：
2012-08
影响因子：
14.9
通讯作者：
Adamiak RW
中科院分区：
文献类型：
--
作者：
Popenda M;Szachniuk M;Antczak M;Purzycka KJ;Lukasiak P;Bartol N;Blazewicz J;Adamiak RW
要了解RNA在活细胞中发挥的众多功能，关键取决于对其三维结构的了解。由于实验评估大RNA结构的困难，目前对新的高分辨率结构预测方法的需求很大。我们提出了一种从用户定义的二级结构中全自动预测RNA 3D结构的新方法。这个概念是建立在机器翻译系统上的。翻译引擎在RNA FRABASE数据库上运行，该数据库针对与RNA二级结构和三级结构元素相关的词典而定制。翻译算法非常快。初始3D结构在单个处理器上在几秒钟内组成。该方法确保了高质量的大RNA 3D结构的预测。我们的方法既不需要结构模板，也不需要RNA序列比对，这是比较方法所必需的。这使得能够构建尚未解决的天然和人工RNA结构。该方法是在一个公开可用的，用户友好的服务器RNAComposer中实现的。它以交互模式和批处理模式工作。批处理模式设计用于大规模建模，并接受原子距离约束。目前，该服务器可以构建多达500个残基的RNA结构。
Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.
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