ArticlePloS one2013
Cross-link guided molecular modeling with ROSETTA.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
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105 citing papers in PubMed.
- Ion Mobility Mass Spectrometry Guided Modeling with AlphaFold and Rosetta Improves Protein Complex Structure Prediction.bioRxiv : the preprint server for biology · 2026Article
- Elucidating PTEN conformational dynamics and phosphatase regulation via integrative modeling and mutation prediction.Structure (London, England : 1993) · 2025Article
- Protein Secondary Structure Patterns in Short-Range Cross-Link Atlas.Angewandte Chemie (International ed. in English) · 2025Article
- Deep-learning structure elucidation from single-mutant deep mutational scanning.Nature communications · 2025Article
- HDXRank: A Deep Learning Framework for Ranking Protein Complex Predictions with Hydrogen-Deuterium Exchange Data.Journal of chemical theory and computation · 2025Article
- Mapping the interaction surface between CaNature communications · 2025Article
- Energy Resolved Mass Spectrometry Data from Surfaced Induced Dissociation Improves Prediction of Protein Complex Structure.Analytical chemistry · 2025Article
- Multiple allostery in the regulation of PDGFR beta kinase activities.Acta biochimica et biophysica Sinica · 2024Article
- Dual protection by Bcp1 and Rkm1 ensures incorporation of uL14 into pre-60S ribosomal subunits.The Journal of cell biology · 2024Article
- Chemical cross-linking and mass spectrometry enabled systems-level structural biology.Current opinion in structural biology · 2024Review
- Evidence for a compact σiScience · 2024Article
- Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.Journal of chemical information and modeling · 2024Article
- Hybrid structural modeling of alloantibody binding to human leukocyte antigen with rapid and reproducible cross-linking mass spectrometry.Cell reports methods · 2023Article
- Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver.Briefings in bioinformatics · 2023Article
- A new polymodal gating model of the proton-activated chloride channel.PLoS biology · 2023Article
- Conformational Dynamics of the Activated GLP-1 Receptor-GACS central science · 2023Article
- Cross-linking mass spectrometry for mapping protein complex topologies in situ.Essays in biochemistry · 2023Article
- Structural mass spectrometry approaches to understand multidrug efflux systems.Essays in biochemistry · 2023Review
- Unique interface and dynamics of the complex of HSP90 with a specialized cochaperone AIPL1.Structure (London, England : 1993) · 2023Article
- Probing the E1o-E2o and E1a-E2o Interactions in Binary Subcomplexes of the Human 2-Oxoglutarate Dehydrogenase and 2-Oxoadipate Dehydrogenase Complexes by Chemical Cross-Linking Mass Spectrometry and Molecular Dynamics Simulation.International journal of molecular sciences · 2023Article
45 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods.
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