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首页> 外文期刊>Journal of Molecular Biology >Folding kinetics of large RNAs.
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Folding kinetics of large RNAs.

机译：大RNA的折叠动力学。

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摘要

We introduce here a heuristic approach to kinetic RNA folding that constructs secondary structures by stepwise combination of building blocks. These blocks correspond to subsequences and their thermodynamically optimal structures. These are determined by the standard dynamic programming approach to RNA folding. Folding trajectories are modeled at base-pair resolution using the Morgan-Higgs heuristic and a barrier tree-based heuristic to connect combinations of the local building blocks. Implemented in the program Kinwalker, the algorithm allows co-transcriptional folding and can be used to fold sequences of up to about 1500 nucleotides in length. A detailed comparison with several well-studied examples from the literature, including the delayed folding of bacteriophage cloverleaf structures, the adenine sensing riboswitch, and the hok RNA, shows an excellent agreement of predicted trajectories and experimental evidence. The software is available as part of the ViennaRNA Package.
机译：我们在这里介绍动力学RNA折叠的启发式方法，该方法通过逐步组合构件来构建二级结构。这些嵌段对应于子序列及其热力学最佳结构。这些由RNA折叠的标准动态编程方法确定。折叠轨迹使用Morgan-Higgs启发式算法和基于势垒树的启发式方法以碱基对分辨率建模，以连接本地构建模块的组合。该算法在Kinwalker程序中实现，可实现共转录折叠，并可用于折叠长度最多约1500个核苷酸的序列。与文献中几个经过充分研究的实例进行的详细比较，包括噬菌体三叶草结构的延迟折叠，腺嘌呤感测核糖开关和hok RNA，显示了预测的轨迹和实验证据非常吻合。该软件作为ViennaRNA软件包的一部分提供。

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