ArticleStructure (London, England : 1993)2018
Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry.
Article in Structure (London, England : 1993), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Evaluation of methods for AlphaFold-based integrative modeling.bioRxiv : the preprint server for biology · 2026Article
- The phytoplasma effector, phyllogen, structurally mimics host plant MADS transcription factors.The Journal of biological chemistry · 2026Article
- Improving Protein Structure Prediction Using Integrative Cryo-EM and Ion Mobility Mass Spectrometry Modeling.Journal of chemical theory and computation · 2026Article
- Deciphering photosynthetic protein networks: a crosslinking-MS strategy for studying functional thylakoid membranes.The Plant journal : for cell and molecular biology · 2026Article
- Improving Protein Structure Prediction Using Integrative Cryo-EM and Ion Mobility Mass Spectrometry Modeling.bioRxiv : the preprint server for biology · 2026Article
- Mapping the interaction surface between CaNature communications · 2025Article
- Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.Journal of chemical information and modeling · 2024Article
- Higher-Order Structural Organization of the Mitochondrial Proteome Charted by In Situ Cross-Linking Mass Spectrometry.Molecular & cellular proteomics : MCP · 2023Article
- Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET.Nature communications · 2022Article
- Characterization of protein complexes in extracellular vesicles by intact extracellular vesicle crosslinking mass spectrometry (iEVXL).Journal of extracellular vesicles · 2022Article
- Shape shifting: The multiple conformational substates of the PTEN N-terminal PIPProtein science : a publication of the Protein Society · 2022Article
- Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology.Molecular cell · 2022Review
- Proteomic Approaches to Unravel Mechanisms of Antibiotic Resistance and Immune Evasion of Bacterial Pathogens.Frontiers in medicine · 2022Review
- Review
- Selective cross-linking of coinciding protein assemblies by in-gel cross-linking mass spectrometry.The EMBO journal · 2021Article
- Integrative Mass Spectrometry-Based Approaches for Modeling Macromolecular Assemblies.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Automated Modeling and Validation of Protein Complexes in Cryo-EM Maps.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Structural insights and activating mutations in diverse pathologies define mechanisms of deregulation for phospholipase C gamma enzymes.EBioMedicine · 2020Article
- Article
- The Plasma Factor XIII Heterotetrameric Complex Structure: Unexpected Unequal Pairing within a Symmetric Complex.Biomolecules · 2019Article
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4 authors.
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Abstract
Modeling macromolecular assemblies with restraints from crosslinking mass spectrometry (XL-MS) tends to focus solely on distance violation. Recently, we identified three different modeling features inherent in crosslink data: (1) expected distance between crosslinked residues; (2) violation of the crosslinker's maximum bound; and (3) solvent accessibility of crosslinked residues. Here, we implement these features in a scoring function. cMNXL, and demonstrate that it outperforms the commonlyused crosslink distance violation. We compare the different methods of calculating the distance between crosslinked residues, which shows no significant change in performance when using Euclidean distance compared with the solvent-accessible surface distance. Finally, we create a combined score that incorporates information from 3D electron microscopy maps as well as crosslinking. This achieves, on average, better results than either information type alone and demonstrates the potential of integrative modeling with XL-MS and low-resolution cryoelectron microscopy.
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