使用Vfold预测RNA结构
Predicting RNA Structure with Vfold.
作者信息
Zhao Chenhan, Xu Xiaojun, Chen Shi-Jie
机构信息
Department of Physics, Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
出版信息
Methods Mol Biol. 2017;1654:3-15. doi: 10.1007/978-1-4939-7231-9_1.
Abstract
In order to carry out biological functions, RNA molecules must fold into specific three-dimensional (3D) structures. Current experimental methods to determine RNA 3D structures are expensive and time consuming. With the recent advances in computational biology, RNA structure prediction is becoming increasingly reliable. This chapter describes a recently developed RNA structure prediction software, Vfold, a virtual bond-based RNA folding model. The main features of Vfold are the physics-based loop free energy calculations for various RNA structure motifs and a template-based assembly method for RNA 3D structure prediction. For illustration, we use the yybP-ykoY Orphan riboswitch as an example to show the implementation of the Vfold model in RNA structure prediction from the sequence.
摘要
为了执行生物学功能，RNA分子必须折叠成特定的三维（3D）结构。目前用于确定RNA三维结构的实验方法既昂贵又耗时。随着计算生物学的最新进展，RNA结构预测变得越来越可靠。本章介绍了一种最近开发的RNA结构预测软件Vfold，这是一种基于虚拟键的RNA折叠模型。Vfold的主要特点是针对各种RNA结构基序进行基于物理的无环自由能计算，以及用于RNA三维结构预测的基于模板的组装方法。为了说明，我们以yybP-ykoY孤儿核糖开关为例，展示Vfold模型在从序列进行RNA结构预测中的应用。
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