Topological analysis and interactive visualization of biological networks and protein structures
Topological analysis and interactive visualization of biological networks and protein structures
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DOI：
10.1038/nprot.2012.004
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发表时间：
2012-04-01
期刊：
影响因子：
14.8
通讯作者：
Albrecht, Mario
中科院分区：
文献类型：
--
作者：
Doncheva, Nadezhda T.;Assenov, Yassen;Albrecht, Mario
生物网络和蛋白质结构的计算分析和交互式可视化是深入了解生物过程的常见任务。该协议描述了基于NetworkAnalyzer和Cytoscape（一种流行的网络软件平台）的RINalyzer插件的三个工作流程。NetworkAnalyzer已成为一个标准的Cytoscape工具，用于全面的网络拓扑分析。此外，RINalyzer还提供了探索蛋白质结构中残基相互作用网络的方法。第一个工作流程使用NetworkAnalyzer对生物网络进行拓扑分析。第二个工作流程应用RINalyzer研究蛋白质结构和功能，并计算网络中心性度量。第三个工作流程结合NetworkAnalyzer和RINalyzer来比较残差网络。整个方案可在2小时内完成。
Computational analysis and interactive visualization of biological networks and protein structures are common tasks for gaining insight into biological processes. This protocol describes three workflows based on the NetworkAnalyzer and RINalyzer plug-ins for Cytoscape, a popular software platform for networks. NetworkAnalyzer has become a standard Cytoscape tool for comprehensive network topology analysis. In addition, RINalyzer provides methods for exploring residue interaction networks derived from protein structures. The first workflow uses NetworkAnalyzer to perform a topological analysis of biological networks. The second workflow applies RINalyzer to study protein structure and function and to compute network centrality measures. The third workflow combines NetworkAnalyzer and RINalyzer to compare residue networks. The full protocol can be completed in similar to 2 h.