ArticlePLoS computational biology2017
Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 48 citations in OpenAlex.
- Integrated analysis with iCM-SANS, SAXS and MD simulations for dynamics of multi-domain proteins.Journal of applied crystallography · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Optimal weights and priors in simultaneous fitting of multiple small-angle scattering datasets.Journal of applied crystallography · 2025Article
- SANS Spectra with PLUMED: Implementation and Application to Metainference.Journal of chemical information and modeling · 2023Article
- Generation of unfolded outer membrane protein ensembles defined by hydrodynamic properties.European biophysics journal : EBJ · 2023Article
- Biophysical Approaches for the Characterization of Protein-Metabolite Interactions.Methods in molecular biology (Clifton, N.J.) · 2023Review
- Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations.Scientific reports · 2022Article
- From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output.Frontiers in pharmacology · 2022Review
- Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data.Biophysical journal · 2021Article
- Reconciling Simulations and Experiments With BICePs: A Review.Frontiers in molecular biosciences · 2021Review
- Automatic Bayesian Weighting for SAXS Data.Frontiers in molecular biosciences · 2021Article
- Comprehensive Structural and Thermodynamic Analysis of Prefibrillar WT α-Synuclein and Its G51D, E46K, and A53T Mutants by a Combination of Small-Angle X-ray Scattering and Variational Bayesian Weighting.Journal of chemical information and modeling · 2020Article
- Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering.IUCrJ · 2020Article
- Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data.The Journal of chemical physics · 2020Article
- Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement.Journal of chemical information and modeling · 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
- Extended Experimental Inferential Structure Determination Method in Determining the Structural Ensembles of Disordered Protein States.Communications chemistry · 2020Article
- Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations.PloS one · 2020Article
- Addressing the challenges of modeling the scattering from bottlebrush polymers in solution.Journal of polymer science (2020) · 2020Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small-angle X-ray scattering is an increasingly popular technique used to detect protein structures and ensembles in solution. However, the refinement of structures and ensembles against SAXS data is often ambiguous due to the low information content of SAXS data, unknown systematic errors, and unknown scattering contributions from the solvent. We offer a solution to such problems by combining Bayesian inference with all-atom molecular dynamics simulations and explicit-solvent SAXS calculations. The Bayesian formulation correctly weights the SAXS data versus prior physical knowledge, it quantifies the precision or ambiguity of fitted structures and ensembles, and it accounts for unknown systematic errors due to poor buffer matching. The method further provides a probabilistic criterion for identifying the number of states required to explain the SAXS data. The method is validated by refining ensembles of a periplasmic binding protein against calculated SAXS curves. Subsequently, we derive the solution ensembles of the eukaryotic chaperone heat shock protein 90 (Hsp90) against experimental SAXS data. We find that the SAXS data of the apo state of Hsp90 is compatible with a single wide-open conformation, whereas the SAXS data of Hsp90 bound to ATP or to an ATP-analogue strongly suggest heterogenous ensembles of a closed and a wide-open state.
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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.