xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints
Open accessAbstract
The identification of crosslinks by mass spectrometry has recently been established as an integral part of the hybrid structural analysis of protein complexes and networks. The crosslinking analysis determines distance restraints between two covalently linked amino acids which are typically summarized in a table format that precludes the immediate and comprehensive interpretation of the topological data. xVis displays crosslinks in clear schematic representations in form of a circular, bar or network diagram. The interactive graphs indicate the linkage sites and identification scores, depict the spatial proximity of structurally and functionally annotated protein regions and the evolutionary conservation of amino acids and facilitate clustering of proteins into subcomplexes according to the crosslink density. Furthermore, xVis offers two options for the qualitative assessment of the crosslink identifications by filtering crosslinks according to identification scores or false discovery rates and by displaying the corresponding fragment ion spectrum of each crosslink for the manual validation of the mass spectrometric data. Our web server provides an easy-to-use tool for the fast topological and functional interpretation of distance information on protein complex architectures and for the evaluation of crosslink fragment ion spectra. xVis is available under a Creative Commons Attribution-ShareAlike 4.0 International license at http://xvis.genzentrum.lmu.de/.
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Programs have been developed to analyze and visualize cross-linking data as a network of amino acid nodes, where edges represent a detected cross-link, and organizing clusters of nodes spatially according to subunit is one approach applied in these networks.
“For example, programs have been developed to analyze and visualize cross-linking data as a network of amino acid nodes, where edges represent a detected cross-link (Combe et al., 2015; Courcelles et al., 2017; Grimm et al., 2015; Riffle et al., 2016); organizing clusters of nodes spatially according to subunit is one approach that has been applied in these networks (Figure 5C).”
From Mapping the multiscale structure of biological systems (2021) · cites this paper as Grimm et al., 2015
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- Authors
- Grimm, M., Zimniak, T., Kahraman, A., & Herzog, F.
- Affiliations
- Ludwig-Maximilians-Universität München (DE)
- University of Zurich (CH)
- Corresponding author
- Herzog, Franz
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-05-08
- Volume
- 43
- Issue
- W1
- Pages
- W362-W369
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4489277
- OpenAlex
- W1644001471
- Cited by
- 121
- References
- 30
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 14 · 2023: 9 · 2022: 10 · 2021: 17 · 2020: 17 · 2019: 13 · 2018: 15 · 2017: 11 · 2016: 9 · 2015: 1
- FWCI
- 5.35
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Open access LMU (Ludwid Maxmilian's Universitat Munchen) (submittedVersion, cc-by-sa)
- Funders
- Deutsche Forschungsgemeinschaft (GRK1721)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- crosslinking, distance restraints, protein complexes, protein networks, web server, false discovery rate, fragment ion spectra, evolutionary conservation
- MeSH terms
- Algorithms, Amino Acids, Computer Graphics, Cross-Linking Reagents, Histones, Nucleosomes, Software, Mass Spectrometry, Internet, Chromatin Assembly and Disassembly, Multiprotein Complexes
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