期刊
JOURNAL OF PROTEOME RESEARCH
卷 20, 期 4, 页码 1943-1950出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.0c00957
关键词
protein-protein interaction; structural biology; cross-linking mass spectrometry; Cytoscape; bioinformatics
资金
- Leibniz-SAW program (SAW) [P70/2018]
- Deutsche Forschungsgemeinschaft (DFG
- German Research Foundation) [SFB958/Z03]
- Leibniz Association
This paper introduces XlinkCyNET, an open-source Cytoscape Java plug-in designed for exploring large-scale XL-MS-based protein interaction networks, providing rapid and easy visualization of intra- and interprotein cross-links at the residue level.
Software tools that allow the visualization and analysis of protein interaction networks are essential for studies in systems biology. One of the most popular network visualization tools in biology is Cytoscape, which offers a great selection of plug-ins for the interpretation of network data. Chemical cross-linking coupled to mass spectrometry (XL-MS) is an increasingly important source for protein interaction data; however, to date, no Cytoscape tools are available to analyze XL-MS results. In light of the suitability of the Cytoscape platform and to expand its toolbox, here we introduce XlinkCyNET, an open-source Cytoscape Java plug-in for exploring large-scale XL-MS-based protein interaction networks. XlinkCyNET offers the rapid and easy visualization of intra- and interprotein cross-links in a rectangular-bar style as well as on the 3D structure, allowing the interrogation of protein interaction networks at the residue level. XlinkCyNET is freely available from the Cytoscape App Store (http://apps.cytoscape.org/apps/xlinkcynet) and at the Liu lab webpage (https://www.theliulab.com/software/xlinkcynet).
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