Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
BMC Bioinformatics. 2010 May 6;11:231. doi: 10.1186/1471-2105-11-231.
Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization.
RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl.
RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field.
最近关于 RNA 的新功能的发现，如 RNA 干扰，使得该领域的重要性不断增加。在这方面，深入了解复杂的三维 RNA 结构对于理解它们的新生物学功能至关重要。已经提出了许多生物信息学工具来探索两个主要的结构数据库（PDB、NDB），以便分析 RNA 三级结构的各个方面。这些工具之一是 RNA FRABASE 1.0，这是第一个具有自动搜索 PDB 衍生 RNA 结构中 3D 片段的引擎的可访问数据库。这种搜索是基于用户定义的 RNA 二级结构模式进行的。在本文中，我们介绍并讨论了 RNA FRABASE 2.0。该系统的第二个版本在提供新数据和广泛的新功能方面是该工具的重大扩展。直观操作的网络服务器平台使非常快速的用户定制三维 RNA 片段搜索、它们的多参数构象分析和可视化成为可能。
RNA FRABASE 2.0 存储了 1565 个 PDB 存放的 RNA 结构的信息，包括所有 NMR 模型。RNA FRABASE 2.0 搜索引擎算法在 RNA 序列数据库和新的 RNA 二级结构库上运行，该库以点括号格式编码，扩展后可容纳多链结构，并涵盖在 PDB 文件中坐标缺失的残基。RNA 二级结构库（及其图形）可供使用。通过引入新的工具来制定高级搜索模式和筛选高度流行的三级结构元素，实现了 3D 搜索的高效率。RNA FRABASE 2.0 还存储数据和构象参数，以便提供“即时”结构筛选器来探索三维 RNA 结构。提供了 3D RNA 结构的即时可视化。RNA FRABASE 2.0 可在 http://rnafrabase.cs.put.poznan.pl 免费获得。
RNA FRABASE 2.0 提供了一个新的数据库和强大的搜索引擎，它配备了其他地方不可用的新数据和功能。我们的意图是，这个高级版本的 RNA FRABASE 将引起所有在 RNA 领域工作的研究人员的兴趣。
