ArticleBioinformatics (Oxford, England)2011
Xwalk: computing and visualizing distances in cross-linking experiments.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
- 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
- Structural mechanisms of drebrin-mediated F-actin network modulation.Nature communications · 2026Article
- XL-MS and De Novo Protein Design Identified a Common Motif for TREM2 Binding.bioRxiv : the preprint server for biology · 2026Article
- Integrative Structural Modeling of Intrinsically Disordered Regions in a Human HDAC2 Chromatin Remodeling Complex.bioRxiv : the preprint server for biology · 2026Article
- Integrating diverse experimental information to assist protein complex structure prediction by GRASP.Nature methods · 2025Article
- Tandem association of CLOCK:BMAL1 complexes on DNA enables recruitment of CBP/p300 through multivalent interactions.bioRxiv : the preprint server for biology · 2025Article
- Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.Nucleic acids research · 2025Article
- Protein Secondary Structure Patterns in Short-Range Cross-Link Atlas.Angewandte Chemie (International ed. in English) · 2025Article
- Mapping Hsp104 interactions using cross-linking mass spectrometry.FEBS open bio · 2025Article
- Integrated structural model of the palladin-actin complex using XL-MS, docking, NMR, and SAXS.Protein science : a publication of the Protein Society · 2025Article
- Multiple allostery in the regulation of PDGFR beta kinase activities.Acta biochimica et biophysica Sinica · 2024Article
- Modelling protein complexes with crosslinking mass spectrometry and deep learning.Nature communications · 2024Article
- Dual protection by Bcp1 and Rkm1 ensures incorporation of uL14 into pre-60S ribosomal subunits.The Journal of cell biology · 2024Article
- CLAUDIO: automated structural analysis of cross-linking data.Bioinformatics (Oxford, England) · 2024Article
- Structure and activation of the RING E3 ubiquitin ligase TRIM72 on the membrane.Nature structural & molecular biology · 2023Article
- Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein-protein interactions in the human cell.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Structural insights into the multifunctionality of rabies virus P3 protein.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Lipid membrane mimetics and oligomerization tune functional properties of proteorhodopsin.Biophysical journal · 2023Article
- The structure ofFrontiers in immunology · 2023Article
- Improved Interpretation of Protein Conformational Differences and Ligand Occupancy in Large-Scale Cross-Link Data.Journal of proteome research · 2022Article
24 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
motivationChemical cross-linking of proteins or protein complexes and the mass spectrometry-based localization of the cross-linked amino acids in peptide sequences is a powerful method for generating distance restraints on the substrate's topology.
resultsHere, we introduce the algorithm Xwalk for predicting and validating these cross-links on existing protein structures. Xwalk calculates and displays non-linear distances between chemically cross-linked amino acids on protein surfaces, while mimicking the flexibility and non-linearity of cross-linker molecules. It returns a 'solvent accessible surface distance', which corresponds to the length of the shortest path between two amino acids, where the path leads through solvent occupied space without penetrating the protein surface. AVAILABILITY: Xwalk is freely available as a web server or stand-alone JAVA application at http://www.xwalk.org.
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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.