ArticleJournal of chemical theory and computation2015
Deciphering solution scattering data with experimentally guided molecular dynamics simulations.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- A light-triggered Time-Resolved X-ray Solution Scattering (TR-XSS) workflow with application to protein conformational dynamics.FEBS open bio · 2026Article
- Unlocking the unfolded structure of ubiquitin: Combining time-resolved x-ray solution scattering and molecular dynamics to generate unfolded ensembles.The Journal of chemical physics · 2024Article
- Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures.The journal of physical chemistry. B · 2021Article
- The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer.Molecular therapy. Nucleic acids · 2021Article
- Effect of the abolition of intersubunit salt bridges on allosteric protein structural dynamics.Chemical science · 2021Article
- Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations.The Journal of chemical physics · 2021Article
- Tracking Membrane Protein Dynamics in Real Time.The Journal of membrane biology · 2021Review
- Integrating an Enhanced Sampling Method and Small-Angle X-Ray Scattering to Study Intrinsically Disordered Proteins.Frontiers in molecular biosciences · 2021Article
- Structural Characterization of Biomaterials by Means of Small Angle X-rays and Neutron Scattering (SAXS and SANS), and Light Scattering Experiments.Molecules (Basel, Switzerland) · 2020Review
- 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
- Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations.PloS one · 2020Article
- X-ray snapshots reveal conformational influence on active site ligation during metalloprotein folding.Chemical science · 2019Article
- The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane Proteins.The Journal of membrane biology · 2019Review
- Rapid interpretation of small-angle X-ray scattering data.PLoS computational biology · 2019Article
- A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints.International journal of molecular sciences · 2019Article
- SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes.Scientific reports · 2018Article
- The role of small-angle scattering in structure-based screening applications.Biophysical reviews · 2018Review
- Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics.PLoS computational biology · 2017Article
- SAXS-Oriented Ensemble Refinement of Flexible Biomolecules.Biophysical journal · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Time-resolved X-ray solution scattering is an increasingly popular method to measure conformational changes in proteins. Extracting structural information from the resulting difference X-ray scattering data is a daunting task. We present a method in which the limited but precious information encoded in such scattering curves is combined with the chemical knowledge of molecular force fields. The molecule of interest is then refined toward experimental data using molecular dynamics simulation. Therefore, the energy landscape is biased toward conformations that agree with experimental data. We describe and verify the method, and we provide an implementation in GROMACS.
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Registered trials
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.