ArticleInternational journal of molecular sciences2025
Epitope Mapping with Sidewinder: An XL-MS and Structural Modeling Approach.
Article in International journal of molecular sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Rational selection of antigenic targets for Group A Streptococcus vaccine: updates, challenges and opportunities.NPJ vaccines · 2026Review
- Ion Mobility Mass Spectrometry Guided Modeling with AlphaFold and Rosetta Improves Protein Complex Structure Prediction.bioRxiv : the preprint server for biology · 2026Article
- Methods for the Investigation of Protein-Ligands Interactions.Advances in experimental medicine and biology · 2026Review
- State-of-the-Art and Future Directions in Structural Proteomics.Molecular & cellular proteomics : MCP · 2025Review
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Authors and funding
9 authors.
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Abstract
Antibodies are critical to the host's immune defense against bacterial pathogens. Understanding the mechanisms of antibody-antigen interactions is essential for developing new targeted immunotherapies. Building computational workflows that can identify where an antibody binds its cognate antigen and deconvoluting the interaction interface in a high-throughput manner are critical for advancing this field. Cross-linking mass spectrometry (XL-MS) integrated with structural modeling offers a flexible and high-resolution strategy to map protein-protein interactions from low sample amounts. However, cross-linking and in silico modeling have limitations that require robust analytical workflows to make accurate inferences. In this study, we introduce Sidewinder, a modular high-throughput pipeline combining state-of-the-art computational structural prediction and molecular docking with rapid XL-MS analysis, enabling comprehensive interrogation of antibody-antigen systems. We validated this pipeline on antibodies targeting two
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