RAG-Web：基于 RNA-As-Graphs 的 RNA 结构预测/设计。
RAG-Web: RNA structure prediction/design using RNA-As-Graphs.
机构信息
Department of Chemistry, New York University, New York, NY 10003, USA.
Department of Chemistry, Smith College, Northampton, MA 01063, USA.
出版信息
Bioinformatics. 2020 Jan 15;36(2):647-648. doi: 10.1093/bioinformatics/btz611.
SUMMARY
We launch a webserver for RNA structure prediction and design corresponding to tools developed using our RNA-As-Graphs (RAG) approach. RAG uses coarse-grained tree graphs to represent RNA secondary structure, allowing the application of graph theory to analyze and advance RNA structure discovery. Our webserver consists of three modules: (a) RAG Sampler: samples tree graph topologies from an RNA secondary structure to predict corresponding tertiary topologies, (b) RAG Builder: builds three-dimensional atomic models from candidate graphs generated by RAG Sampler, and (c) RAG Designer: designs sequences that fold onto novel RNA motifs (described by tree graph topologies). Results analyses are performed for further assessment/selection. The Results page provides links to download results and indicates possible errors encountered. RAG-Web offers a user-friendly interface to utilize our RAG software suite to predict and design RNA structures and sequences.
AVAILABILITY AND IMPLEMENTATION
The webserver is freely available online at: http://www.biomath.nyu.edu/ragtop/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
我们推出了一个用于 RNA 结构预测和设计的网络服务器，该服务器对应于我们使用 RNA-As-Graphs (RAG) 方法开发的工具。RAG 使用粗粒度的树图来表示 RNA 二级结构，允许应用图论来分析和推进 RNA 结构发现。我们的网络服务器由三个模块组成：(a) RAG Sampler：从 RNA 二级结构中采样树图拓扑结构，以预测相应的三级拓扑结构，(b) RAG Builder：从 RAG Sampler 生成的候选图中构建三维原子模型，以及 (c) RAG Designer：设计折叠成新 RNA 基序（由树图拓扑结构描述）的序列。结果分析用于进一步评估/选择。结果页面提供了下载结果的链接，并指出可能遇到的错误。RAG-Web 提供了一个用户友好的界面，可用于利用我们的 RAG 软件套件来预测和设计 RNA 结构和序列。
可用性和实现
该网络服务器可免费在线使用：http://www.biomath.nyu.edu/ragtop/。
补充信息
补充数据可在 Bioinformatics 在线获得。
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