ArticleProtein science : a publication of the Protein Society2020
PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system.
Article in Protein science : a publication of the Protein Society, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
- Unified down-stream analysis of crosslinking mass spectrometry results with pyXLMS.Nature communications · 2026Article
- DirectContacts2: a wiring diagram of human physical protein interactions.Nature communications · 2026Article
- Structural, Evolutionary, and Regulatory Divergence ofPlants (Basel, Switzerland) · 2026Article
- Prognostic Significance and Immune Landscape of Migrasome-Related Genes in Pancreatic Cancer.Applied biochemistry and biotechnology · 2026Article
- Prenatal Diagnosis of Autosomal Recessive Primary Microcephaly Type 2 Caused by Compound Heterozygous WDR62 Variants in a Family With Two Recurrent Cases.Molecular genetics & genomic medicine · 2026Article
- Predicting the protein interaction landscape of a free-living bacterium with pooled-AlphaFold3.Molecular systems biology · 2026Article
- RPA directly stimulates Mer3 helicase processivity to ensure normal crossover formation in meiosis.Nature communications · 2026Article
- The crucial but insufficient role of E2s domain's residues 490 and 492 in determining the host tropism of hepatitis E virus.Nature communications · 2026Article
- Article
- Allosteric activation of a cell-type-specific GPR120 inhibits amyloid pathology of Alzheimer's disease.Nature aging · 2026Article
- Licorice-derived prenylated chalcones alleviate knee osteoarthritis via multi-target modulation of PI3K-Akt, MAPK and HIF-1α signaling: an integrative UPLC-Q-TOF-MS/MS, network pharmacology and molecular dynamics study.Frontiers in bioinformatics · 2026Article
- Liubao tea as a functional fermented food: multi-omics insights into its modulation of lymphatic endothelial cell metabolism.Frontiers in nutrition · 2026Article
- Integrative profiling of lactylation reveals prognostic biomarkers and an immunosuppressive niche in acute myeloid leukemia.Frontiers in immunology · 2026Article
- A Comprehensive Analysis of the ITIH Family Across Multiple Cancer Types and an Initial Investigation of ITIH1 in Gastric Cancer.Current medicinal chemistry · 2026Article
- Towards a universal cross-linking mass spectrometry approach for protein structure analysis with homo-bi-functional photo-activatable cross-linkers.Communications biology · 2025Article
- Article
- Rescuing fertility: C-Phycocyanin prevents ovarian damage through NRF2-mediated ferroptosis pathways in polycystic ovary syndrome models.Zoological research · 2025Article
- The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking.Nature structural & molecular biology · 2025Article
- State-of-the-Art and Future Directions in Structural Proteomics.Molecular & cellular proteomics : MCP · 2025Review
- Structural basis of RECQL5-induced RNA polymerase II transcription braking and subsequent reactivation.Nature structural & molecular biology · 2025Article
16 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Chemical crosslinking-mass spectrometry (XL-MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL-MS data yield inter-residue restraints that can be compared with high-resolution structural data. Distances greater than the crosslinker spacer-arm can reveal lowly populated "excited" states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of structural data. Despite increasing uptake of XL-MS, there are few tools to enable rapid and facile mapping of XL-MS data onto high-resolution structures or structural models. PyXlinkViewer is a user-friendly plugin for PyMOL v2 that maps intra-protein, inter-protein, and dead-end crosslinks onto protein structures/models and automates the calculation of inter-residue distances for the detected crosslinks. This enables rapid visualization of XL-MS data, assessment of whether a set of detected crosslinks is congruent with structural data, and easy production of high-quality images for publication.
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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.