Facultad de Ciencias Biologicas, Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Alameda 340, Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Santiago, Chile and Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 19 st. south, Birmingham, AL 35249, USA.
Bioinformatics. 2013 Oct 15;29(20):2649-50. doi: 10.1093/bioinformatics/btt441. Epub 2013 Aug 7.
The understanding of the biological role of RNA molecules has changed. Although it is widely accepted that RNAs play important regulatory roles without necessarily coding for proteins, the functions of many of these non-coding RNAs are unknown. Thus, determining or modeling the 3D structure of RNA molecules as well as assessing their accuracy and stability has become of great importance for characterizing their functional activity. Here, we introduce a new web application, WebRASP, that uses knowledge-based potentials for scoring RNA structures based on distance-dependent pairwise atomic interactions. This web server allows the users to upload a structure in PDB format, select several options to visualize the structure and calculate the energy profile. The server contains online help, tutorials and links to other related resources. We believe this server will be a useful tool for predicting and assessing the quality of RNA 3D structures.
The web server is available at http://melolab.org/webrasp. It has been tested on the most popular web browsers and requires Java plugin for Jmol visualization.
人们对 RNA 分子的生物学作用的理解已经发生了变化。虽然人们普遍认为，RNA 在不编码蛋白质的情况下也发挥着重要的调节作用，但许多这些非编码 RNA 的功能仍然未知。因此，确定或模拟 RNA 分子的三维结构，并评估其准确性和稳定性，对于表征其功能活性变得非常重要。在这里，我们介绍了一个新的网络应用程序 WebRASP，它使用基于知识的势能来根据距离相关的成对原子相互作用对 RNA 结构进行评分。该网络服务器允许用户上传 PDB 格式的结构，选择几个选项来可视化结构并计算能量分布。该服务器包含在线帮助、教程和其他相关资源的链接。我们相信，该服务器将成为预测和评估 RNA 三维结构质量的有用工具。
该网络服务器可在 http://melolab.org/webrasp 上访问。它已经在最流行的网络浏览器上进行了测试，并且需要 Java 插件才能进行 Jmol 可视化。
