ArticleJournal of structural biology2015
Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures.
Article in Journal of structural biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
101 citing papers in PubMed.
- A conserved GTPase complex gates exocytosis for defence and parasitism across alveolates.Nature microbiology · 2026Article
- The N-terminus of alpha-1 giardin, a parasitic annexin orthologue, is essential for oligomerization and lipid-binding activity.PLoS pathogens · 2026Article
- Scalable discovery of homomeric protein-protein interactions from cross-linking mass spectrometry data with CLAUDIO 2.0.Protein science : a publication of the Protein Society · 2026Article
- gapTrick-structural characterization of protein-protein interactions using AlphaFold.Bioinformatics (Oxford, England) · 2025Article
- Structure of the nucleosome-bound human BCL7A.Nucleic acids research · 2025Article
- Structural basis of thymidine-rich DNA recognition by Drosophila P75 PWWP domain.Communications biology · 2025Article
- Structural basis for lipid transfer by the ATG2A-ATG9A complex.Nature structural & molecular biology · 2025Article
- Architecture of the Sap S-layer ofProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler.Cell · 2024Article
- Structural basis of the human transcriptional Mediator regulated by its dissociable kinase module.Molecular cell · 2024Article
- Structure of the human TIP60 complex.Nature communications · 2024Article
- Article
- CLAUDIO: automated structural analysis of cross-linking data.Bioinformatics (Oxford, England) · 2024Article
- Structural basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair.Nature structural & molecular biology · 2024Article
- Probing Protein Complexes Composition, Stoichiometry, and Interactions by Peptide-Based Mass Spectrometry.Advances in experimental medicine and biology · 2024Article
- Structure of the transcribing RNA polymerase II-Elongin complex.Nature structural & molecular biology · 2023Article
- Hybrid structural modeling of alloantibody binding to human leukocyte antigen with rapid and reproducible cross-linking mass spectrometry.Cell reports methods · 2023Article
- Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism.Nature communications · 2023Article
- Structure of nascent 5S RNPs at the crossroad between ribosome assembly and MDM2-p53 pathways.Nature structural & molecular biology · 2023Article
- Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques. Cross-linking mass spectrometry (XL-MS) identifies proximal protein residues and thus is increasingly used to map protein interactions and determine the relative orientation of subunits within the structure of protein complexes. To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures. Xlink Analyzer enables automatic visualization of cross-links, identifies cross-links violating spatial restraints, calculates violation statistics, maps chemically modified surfaces, and allows interactive manipulations that facilitate analysis of XL-MS data and aid designing new experiments. We demonstrate these features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex. Xlink Analyzer is implemented as a plugin to UCSF Chimera, a standard structural biology software tool, and thus enables seamless integration of XL-MS data with, e.g. fitting of X-ray structures to EM maps. Xlink Analyzer is available for download at http://www.beck.embl.de/XlinkAnalyzer.html.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.