XlinkCyNET is an open-source Cytoscape plugin that generates residue-to-residue connections provided by XL-MS in protein interaction networks. Importantly, it provides an interactive interface for the exploration of cross-links and offers various options to display protein domains. XlinkCyNET works well in complex networks containing thousands of proteins.
A video (https://www.youtube.com/embed/uLuJ7RlFb3I?rel=0&showinfo=0) demonstrating how the application works can be found on the software website (https://www.theliulab.com/software/xlinkcynet). A detailed tutorial, which explains step by step the functionality of all parameters is available at Protocol Exchange (http://dx.doi.org/10.21203/rs.3.pex-1172/v1).
XlinkCyNET can be downloaded at Cytoscape App Store (https://apps.cytoscape.org/apps/xlinkcynet)
↪ Visualize protein-protein interaction network based on cross-linking mass spectrometry data
↪ Apply a residue-to-residue layout to a Cytoscape interaction network
↪ Annotate protein domains to all nodes in the network
↪ Map cross-links on high-resolution structures through PyMOL.
↪ AlphaFold is possible to be used to retrieve protein structures.
↪ XlinkCyNET supports Cytoscape Automation from both commands and CyREST by providing ten different commands:
Don't hesitate to send us any comments, questions or bug reports to: diogobor [at] gmail [dot] com
Any feedback is welcomed!
Have fun! :)