ArticleBioinformatics (Oxford, England)2012
A method for integrative structure determination of protein-protein complexes.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Integrative Structural Modeling of Intrinsically Disordered Regions in a Human HDAC2 Chromatin Remodeling Complex.bioRxiv : the preprint server for biology · 2026Article
- A highly sensitive protein-RNA cross-linking mass spectrometry workflow with enhanced structural modeling potential.Nucleic acids research · 2025Article
- Epitope Mapping Using Yeast Display and Next Generation Sequencing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence.Molecules (Basel, Switzerland) · 2024Review
- Evidence for a compact σiScience · 2024Article
- Integrative structure determination reveals functional global flexibility for an ultra-multimodular arabinanase.Communications biology · 2022Article
- Review
- Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies.Cell systems · 2021Article
- Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2.Science (New York, N.Y.) · 2020Article
- Genetic interaction mapping informs integrative structure determination of protein complexes.Science (New York, N.Y.) · 2020Article
- Combining Experimental Data and Computational Methods for the Non-Computer Specialist.Molecules (Basel, Switzerland) · 2020Review
- Neighborhood Preference of Amino Acids in Protein Structures and its Applications in Protein Structure Assessment.Scientific reports · 2020Article
- Proper evaluation of chemical cross-linking-based spatial restraints improves the precision of modeling homo-oligomeric protein complexes.BMC bioinformatics · 2019Article
- Archiving and disseminating integrative structure models.Journal of biomolecular NMR · 2019Article
- Single-Molecule 3D Images of "Hole-Hole" IgG1 Homodimers by Individual-Particle Electron Tomography.Scientific reports · 2019Article
- Chemical cross-linking in the structural analysis of protein assemblies.Methods (San Diego, Calif.) · 2018Review
- Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.Journal of molecular biology · 2018Article
- Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.Biophysical journal · 2018Article
- Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.Journal of structural biology · 2017Article
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17 authors.
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Abstract
motivationStructural characterization of protein interactions is necessary for understanding and modulating biological processes. On one hand, X-ray crystallography or NMR spectroscopy provide atomic resolution structures but the data collection process is typically long and the success rate is low. On the other hand, computational methods for modeling assembly structures from individual components frequently suffer from high false-positive rate, rarely resulting in a unique solution.
resultsHere, we present a combined approach that computationally integrates data from a variety of fast and accessible experimental techniques for rapid and accurate structure determination of protein-protein complexes. The integrative method uses atomistic models of two interacting proteins and one or more datasets from five accessible experimental techniques: a small-angle X-ray scattering (SAXS) profile, 2D class average images from negative-stain electron microscopy micrographs (EM), a 3D density map from single-particle negative-stain EM, residue type content of the protein-protein interface from NMR spectroscopy and chemical cross-linking detected by mass spectrometry. The method is tested on a docking benchmark consisting of 176 known complex structures and simulated experimental data. The near-native model is the top scoring one for up to 61% of benchmark cases depending on the included experimental datasets; in comparison to 10% for standard computational docking. We also collected SAXS, 2D class average images and 3D density map from negative-stain EM to model the PCSK9 antigen-J16 Fab antibody complex, followed by validation of the model by a subsequently available X-ray crystallographic structure.
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