SIRET Research Group, Department of Software Engineering, FMP, Charles University in Prague, 11800 Czech Republic.
Bioinformatics. 2012 Jul 15;28(14):1858-64. doi: 10.1093/bioinformatics/bts301. Epub 2012 May 18.
Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their 3D structures. Although a structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. However, the growth of the number of large RNAs deposited in the PDB database calls for the development of fast and accurate methods for analyzing their structures, as well as for rapid similarity searches in databases.
In this article a novel algorithm for an RNA structural comparison SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) is introduced. SETTER uses a pairwise comparison method based on 3D similarity of the so-called generalized secondary structure units. For each pair of structures, SETTER produces a distance score and an indication of its statistical significance. SETTER can be used both for the structural alignments of structures that are already known to be homologous, as well as for 3D structure similarity searches and functional annotation. The algorithm presented is both accurate and fast and does not impose limits on the size of aligned RNA structures.
The SETTER program, as well as all datasets, is freely available from http://siret.cz/hoksza/projects/setter/.
理解 RNA 分子的结构和功能需要用于比较和分析其 3D 结构的方法。虽然短 RNA 的结构比对在合理的时间内是可行的，但大型结构则是一个更大的挑战。然而，大量储存在 PDB 数据库中的大型 RNA 的数量的增长要求开发快速且准确的方法来分析它们的结构，以及在数据库中进行快速相似性搜索。
本文介绍了一种新的 RNA 结构比较算法 SETTER（基于二级结构的三级结构相似性算法）。SETTER 使用基于所谓的广义二级结构单元的 3D 相似性的成对比较方法。对于每一对结构，SETTER 都会生成一个距离得分及其统计学意义的指示。SETTER 可用于已经知道同源的结构的结构比对，以及 3D 结构相似性搜索和功能注释。所提出的算法既准确又快速，并且不对对齐的 RNA 结构的大小施加限制。
SETTER 程序以及所有数据集均可从 http://siret.cz/hoksza/projects/setter/ 免费获得。
