xiNET: Cross-link Network Maps With Residue Resolution

Abstract

UNLABELLED: xiNET is a visualization tool for exploring cross-linking/mass spectrometry results. The interactive maps of the cross-link network that it generates are a type of node-link diagram. In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures. AVAILABILITY: xiNET is open source, released under the Apache version 2 license. Results can be viewed by uploading data to http://crosslinkviewer.org/ or by downloading the software from http://github.com/colin-combe/crosslink-viewer and running it locally.

Cited by papers we hold 8

• Structural host-virus interactome profiling of intact infected cells · 2025
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• Cooperation between bHLH transcription factors and histones for DNA access · 2023
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• A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6 · 2022
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• Structural basis of human transcription–DNA repair coupling · 2021
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• Reliable identification of protein-protein interactions by crosslinking mass spectrometry · 2021
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• PyXlinkViewer : A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system · 2020
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• Structural basis of TFIIH activation for nucleotide excision repair · 2019
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• The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for coexisting respiratory supercomplexes · 2018
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