Auron P E, Rindone W P, Vary C P, Celentano J J, Vournakis J N
Nucleic Acids Res. 1982 Jan 11;10(1):403-19. doi: 10.1093/nar/10.1.403.
A brief survey of computer algorithms that have been developed to generate predictions of the secondary structures of RNA molecules is presented. Two particular methods are described in some detail. The first utilizes a thermodynamic energy minimization algorithm that takes into account the likelihood that short-range folding tends to be favored over long-range interactions. The second utilizes an interactive computer graphic modelling algorithm that enables the user to consider thermodynamic criteria as well as structural data obtained by nuclease susceptibility, chemical reactivity and phylogenetic studies. Examples of structures for prokaryotic 16S and 23S ribosomal RNAs, several eukaryotic 5S ribosomal RNAs and rabbit beta-globin messenger RNA are presented as case studies in order to describe the two techniques. Anm argument is made for integrating the two approaches presented in this paper, enabling the user to generate proposed structures using thermodynamic criteria, allowing interactive refinement of these structures through the application of experimentally derived data.
本文简要介绍了已开发出的用于预测RNA分子二级结构的计算机算法。详细描述了两种特定方法。第一种方法利用热力学能量最小化算法，该算法考虑了短程折叠比长程相互作用更受青睐的可能性。第二种方法利用交互式计算机图形建模算法，该算法使用户能够考虑热力学标准以及通过核酸酶敏感性、化学反应性和系统发育研究获得的结构数据。作为案例研究，展示了原核16S和23S核糖体RNA、几种真核5S核糖体RNA以及兔β-珠蛋白信使RNA的结构示例，以描述这两种技术。本文提出了将这两种方法相结合的观点，即使用户能够根据热力学标准生成提议的结构，并通过应用实验得出的数据对这些结构进行交互式优化。
