ArticleJournal of chemical theory and computation2017
Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Information theory optimization of signals from small-angle scattering measurements.Biophysical journal · 2025Article
- Autonomous screening of complex phase spaces using Bayesian optimization for SAXS measurements.Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment · 2023Article
- Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action.The international journal of high performance computing applications · 2022Article
- Characterisation of HOIP RBR E3 ligase conformational dynamics using integrative modelling.Scientific reports · 2022Article
- Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations.Scientific reports · 2022Article
- Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein.PLoS computational biology · 2020Article
- NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains.International journal of molecular sciences · 2020Article
- Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data.The Journal of chemical physics · 2020Article
- Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics.Journal of chemical theory and computation · 2020Article
- Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution.PLoS computational biology · 2020Article
- Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.Current opinion in structural biology · 2019Review
- BEES: Bayesian Ensemble Estimation from SAS.Biophysical journal · 2019Article
- Bayesian inference of protein conformational ensembles from limited structural data.PLoS computational biology · 2018Article
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6 authors.
Funding
Abstract
Small-angle X-ray scattering (SAXS) has become an increasingly popular technique for characterizing the solution ensemble of flexible biomolecules. However, data resulting from SAXS is typically low-dimensional and is therefore difficult to interpret without additional structural knowledge. In theory, molecular dynamics (MD) trajectories can provide this information, but conventional simulations rarely sample the complete ensemble. Here, we demonstrate that accelerated MD simulations can be used to produce higher quality models in shorter time scales than standard simulations, and we present an iterative Bayesian Monte Carlo method that is able to identify multistate ensembles without overfitting. This methodology is applied to several ubiquitin trimers to demonstrate the effect of linkage type on the solution states of the signaling protein. We observe that the linkage site directly affects the solution flexibility of the trimer and theorize that this difference in plasticity contributes to their disparate roles in vivo.
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