期刊
JOURNAL OF MOLECULAR BIOLOGY
卷 351, 期 1, 页码 26-38出版社
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2005.06.024
关键词
RNA structure; structural library; nucleotide doublet; clustering; computational
资金
- NIGMS NIH HHS [R01 GM041455, GM41455, R37 GM041455, R37 GM041455-17] Funding Source: Medline
The rapidly increasing wealth of structural information on RNA and knowledge of its varying roles in biology have facilitated the study of RNA structure using computational methods. Here, we present a new method to describe RNA structure based on nucleotide doublets, where a doublet is any two nucleotides in a structure. We restrict our search to doublets that are close together in space, but not necessarily in sequence, and obtain doublet libraries of various sizes by clustering a large set of doublets taken from a data set of high-resolution RNA structures. We demonstrate that these libraries are able to both capture structural features present in RNA and fit local RNA structure with a high level of accuracy. Libraries ranging in size from ten to 100 doublets are examined, and a detailed analysis shows that a library with as few as 30 doublets is sufficient to capture the most common structural features, while larger libraries would be more appropriate for accurate modeling. We anticipate many uses for these libraries, from annotation to structure refinement and prediction. (c) 2005 Elsevier Ltd. All rights reserved.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据