xiNET: cross-link network maps with residue resolution.
Bottom Line: 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. xiNET is open source, released under the Apache version 2 license.
Affiliation: From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;Show MeSH
Related in: MedlinePlus
Mentions: This is illustrated in Fig. 1, which shows six node-link representations of the same CLMS data. For simplicity, we use only the inter-protein cross-links from this dataset, omitting self-links (links back to a protein of the same type). The data is taken from Chen et al. (1), who investigated the structure of the RNA polymerase II-TFIIF complex. Essential to their conclusions is CLMS evidence for the locations of dimerization domains between Tfg1 and Tgf2.
Affiliation: From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;