ArticleProtein science : a publication of the Protein Society2021
MMM: Integrative ensemble modeling and ensemble analysis.
Article in Protein science : a publication of the Protein Society, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 37 citations in OpenAlex.
- Large-scale protein conformational transitions revealed by weighted ensemble simulations and EPR.Chemical science · 2026Article
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- Hidden protein disorder: Deciphering the structural organisation and dynamics of a non-canonical CP12 from the diatom Thalassiosira pseudonana.The FEBS journal · 2025Article
- State-of-the-Art and Future Directions in Structural Proteomics.Molecular & cellular proteomics : MCP · 2025Review
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- Temperature-Dependent Rotation of Protonated Methyl Groups in Otherwise Deuterated Proteins Modulates DEER Distance Distributions.Applied magnetic resonance · 2025Article
- Article
- Protein ensemble modeling and analysis with MMMx.Protein science : a publication of the Protein Society · 2024Article
- Modeling of Cu(II)-based protein spin labels using rotamer libraries.Physical chemistry chemical physics : PCCP · 2024Article
- Lateral gating mechanism and plasticity of the β-barrel assembly machinery complex in micelles andPNAS nexus · 2024Article
- Conformational Heterogeneity of β-Barrel Membrane Proteins Observed In Situ Using Orthogonal Spin Labels and Pulsed ESR Spectroscopy.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Revealing the DNA Binding Modes of CsoR by EPR Spectroscopy.ACS omega · 2023Article
- A novel approach to modeling side chain ensembles of the bifunctional spin label RX.bioRxiv : the preprint server for biology · 2023Article
- GdJournal of the American Chemical Society · 2023Article
- Integration of Nanometer-Range Label-to-Label Distances and Their Distributions into Modelling Approaches.Biomolecules · 2022Review
- Combined Pulsed Electron Double Resonance EPR and Molecular Dynamics Investigations of Calmodulin Suggest Effects of Crowding Agents on Protein Structures.Biochemistry · 2022Article
- Large-Scale Conformational Changes of FhaC Provide Insights Into the Two-Partner Secretion Mechanism.Frontiers in molecular biosciences · 2022Article
- Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules.Journal of the American Chemical Society · 2021Article
- MMM: Integrative ensemble modeling and ensemble analysis.Protein science : a publication of the Protein Society · 2021Article
- Characterization of Weak Protein Domain Structure by Spin-Label Distance Distributions.Frontiers in molecular biosciences · 2021Article
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1 author at 1 institution in 1 country.
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Abstract
Proteins and their complexes can be heterogeneously disordered. In ensemble modeling of such systems with restraints from several experimental techniques the following problems arise: (a) integration of diverse restraints obtained on different samples under different conditions; (b) estimation of a realistic ensemble width; (c) sufficient sampling of conformational space; (d) representation of the ensemble by an interpretable number of conformers; (e) recognition of weak order with site resolution. Here, I introduce several tools that address these problems, focusing on utilization of distance distribution information for estimating ensemble width. The RigiFlex approach integrates such information with high-resolution structures of ordered domains and small-angle scattering data. The EnsembleFit module provides moderately sized ensembles by fitting conformer populations and discarding conformers with low population. EnsembleFit balances the loss in fit quality upon combining restraint subsets from different techniques. Pair correlation analysis for residues and local compaction analysis help in feature detection. The RigiFlex pipeline is tested on data simulated from the structure 70 kDa protein-RNA complex RsmE/RsmZ. It recovers this structure with ensemble width and difference from ground truth both being on the order of 4.2 Å. EnsembleFit reduces the ensemble of the proliferating-cell-nuclear-antigen-associated factor p15
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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.