模拟 RNA 有序折叠的动力学。

Simulation of Folding Kinetics for Aligned RNAs.

机构信息

Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.

Institute of Biochemical Engineering, Computational Biology group, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.

出版信息

Genes (Basel). 2021 Feb 26;12(3):347. doi: 10.3390/genes12030347.

DOI:10.3390/genes12030347

PMID:33652983

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7996734/

Abstract

Studying the folding kinetics of an RNA can provide insight into its function and is thus a valuable method for RNA analyses. Computational approaches to the simulation of folding kinetics suffer from the exponentially large folding space that needs to be evaluated. Here, we present a new approach that combines structure abstraction with evolutionary conservation to restrict the analysis to common parts of folding spaces of related RNAs. The resulting algorithm can recapitulate the folding kinetics known for single RNAs and is able to analyse even long RNAs in reasonable time. Our program RNAliHiKinetics is the first algorithm for the simulation of consensus folding kinetics and addresses a long-standing problem in a new and unique way.

摘要

研究 RNA 的折叠动力学可以深入了解其功能，因此是 RNA 分析的一种有价值的方法。用于模拟折叠动力学的计算方法受到需要评估的指数级大折叠空间的限制。在这里，我们提出了一种新方法，该方法将结构抽象与进化保守性相结合，将分析限制在相关 RNA 的折叠空间的常见部分。由此产生的算法可以再现单个 RNA 的折叠动力学，并能够在合理的时间内分析甚至长的 RNA。我们的程序 RNAliHiKinetics 是第一个用于模拟共识折叠动力学的算法，它以一种新的、独特的方式解决了一个长期存在的问题。