ArticleJournal of chemical theory and computation2020
Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Atomic resolution ensembles of intrinsically disordered proteins with Alphafold.Nature communications · 2026Article
- Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.Nature communications · 2025Article
- Combining simulations and experiments - a perspective on maximum entropy methods.Physical chemistry chemical physics : PCCP · 2025Review
- Article
- Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference.PLoS computational biology · 2024Article
- Cryo-electron Microscopy and Molecular Modeling Methods to Characterize the Dynamics of Tau Bound to Microtubules.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations.Journal of chemical theory and computation · 2023Article
- Determination of the Structure and Dynamics of the Fuzzy Coat of an Amyloid Fibril of IAPP Using Cryo-Electron Microscopy.Biochemistry · 2023Article
- Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations.Scientific reports · 2022Article
- Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields.Communications chemistry · 2022Review
- Modeling the native ensemble of PhuS using enhanced sampling MD and HDX-ensemble reweighting.Biophysical journal · 2021Article
- Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures.The journal of physical chemistry. B · 2021Article
- Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles.Nucleic acids research · 2021Article
- How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case.Frontiers in molecular biosciences · 2021Article
- Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods.Frontiers in molecular biosciences · 2021Article
- Automatic Bayesian Weighting for SAXS Data.Frontiers in molecular biosciences · 2021Article
- Liquid-Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus-Host Interactions.International journal of molecular sciences · 2020Review
- Combining Experimental Data and Computational Methods for the Non-Computer Specialist.Molecules (Basel, Switzerland) · 2020Review
- The dynamics of linear polyubiquitin.Science advances · 2020Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Small-angle X-ray scattering (SAXS) experiments provide low-resolution but valuable information about the dynamics of biomolecular systems, which could be ideally integrated into molecular dynamics (MD) simulations to accurately determine conformational ensembles of flexible proteins. The applicability of this strategy is hampered by the high computational cost required to calculate scattering intensities from three-dimensional structures. We previously presented a hybrid resolution method that makes atomistic SAXS-restrained MD simulation feasible by adopting a coarse-grained approach to efficiently back-calculate scattering intensities; here, we extend this technique, applying it in the framework of metainference with the aim to investigate the dynamical behavior of flexible biomolecules. The efficacy of the method is assessed on the K63-diubiquitin, showing that the inclusion of SAXS restraints is effective in generating a reliable conformational ensemble, improving the agreement with independent experimental data.
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