Finding the Direct Optimal RNA Barrier Energy and Improving Pathways with an Arbitrary Energy Model
Finding the Direct Optimal RNA Barrier Energy and Improving Pathways with an Arbitrary Energy Model
复制标题
寻找直接最佳 RNA 屏障能量并利用任意能量模型改进途径
DOI：
10.1093/bioinformatics/btaa469
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发表时间：
2020
期刊：
影响因子：
5.8
通讯作者：
Goro Terai and Kiyoshi Asai
中科院分区：
文献类型：
--
作者：
Hiroki Takizawa;Junichi Iwakiri;Goro Terai and Kiyoshi Asai
RNA折叠动力学在RNA分子的生物学功能中起着重要的作用。研究RNA分子动力学行为的一个重要目标是寻找能垒最低的折叠途径。为了这个目的，大多数现有的方法使用的qualitistics，因为可能的途径的数量是巨大的，即使只有最短的（直接）折叠pathways被认为是.ResultsIn这项研究中，我们提出了一种新的方法，使用最好的优先搜索策略，有效地计算直接途径的最小势垒能的精确解。使用我们的方法，我们可以在汉明距离为20的范围内找到精确的直接路径，而以前的方法甚至错过了精确的短路径。此外，我们的方法可以用来改善现有的方法探索间接pathways.Availability和implementationThe源代码和数据集创建和使用本研究可在https://github.com/eukaryo/czno.Supplementary信息补充数据可在Bioinformaticsonline。
MotivationRNA folding kinetics plays an important role in the biological functions of RNA molecules. An important goal in the investigation of the kinetic behavior of RNAs is to find the folding pathway with the lowest energy barrier. For this purpose, most of the existing methods use heuristics because the number of possible pathways is huge even if only the shortest (direct) folding pathways are considered.ResultsIn this study, we propose a new method using a best-first search strategy to efficiently compute the exact solution of the minimum barrier energy of direct pathways. Using our method, we can find the exact direct pathways within a Hamming distance of 20, whereas the previous methods even miss the exact short pathways. Moreover, our method can be used to improve the pathways found by existing methods for exploring indirect pathways.Availability and implementationThe source code and datasets created and used in this research are available at https://github.com/eukaryo/czno.Supplementary informationSupplementary data are available atBioinformaticsonline.