xiNET: cross-link network maps with residue resolution
Open accessAbstract
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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
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 Combe et al., 2015
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
The citation lists haven’t been fetched yet
References 28 · Cited by 296
- Authors
- Combe, C. W., Fischer, L., & Rappsilber, J.
- Affiliations
- Wellcome Centre for Cell Biology (GB)
- Corresponding author
- Rappsilber, Juri
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2015-04
- Volume
- 14
- Issue
- 4
- Pages
- 1137-1147
- ISSN
- 1535-9476 (ISSN-L)
- PMC
- PMC4390258
- OpenAlex
- W2053706533
- Cited by
- 296
- References
- 28
- Citations by year
- 2026: 25 · 2025: 23 · 2024: 25 · 2023: 26 · 2022: 26 · 2021: 47 · 2020: 23 · 2019: 30 · 2018: 26 · 2017: 20 · 2016: 17 · 2015: 8
- FWCI
- 10.56
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular & Cellular Proteomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Funders
- Wellcome Trust (103139, 091020, 103139/Z/13/Z, 084229, 092076)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- crosslinking, node-link diagrams, protein domains, interactive visualization
- MeSH terms
- Amino Acids, Cross-Linking Reagents, Software, Mass Spectrometry, Protein Structure, Tertiary, Transcription Factors, TFII, Protein Multimerization, Protein Interaction Maps
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
