ArticleThe Journal of chemical physics2014
Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids.
Article in The Journal of chemical physics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 41 citations in OpenAlex.
- Fast calculation of small-angle scattering profiles of dense protein solutions modeled at the all-atom level.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Revealing the Solution Conformation and Hydration Structure of Type I Tropocollagen Using X-ray Scattering and Molecular Dynamics Simulation.Biomacromolecules · 2025Article
- Computation of X-ray and Neutron Scattering Patterns to Benchmark Atomistic Simulations against Experiments.International journal of molecular sciences · 2024Article
- Fitting high-resolution electron density maps from atomic models to solution scattering data.Biophysical journal · 2023Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles.Nucleic acids research · 2021Article
- Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering.IUCrJ · 2020Article
- Salt Dependence of A-Form RNA Duplexes: Structures and Implications.The journal of physical chemistry. B · 2019Article
- Theory and simulations for RNA folding in mixtures of monovalent and divalent cations.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Structural Analysis of Biomolecules through a Combination of Mobility Capillary Electrophoresis and Mass Spectrometry.ACS omega · 2019Article
- Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.Biophysical journal · 2018Article
- X-ray Scattering Studies of Protein Structural Dynamics.Chemical reviews · 2017Review
- Visualizing single-stranded nucleic acids in solution.Nucleic acids research · 2017Article
- Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA.Journal of chemical theory and computation · 2017Article
- How accurate are accurate force-fields for B-DNA?Nucleic acids research · 2017Article
- Counting the ions surrounding nucleic acids.Nucleic acids research · 2017Article
- Simultaneous analysis of enzyme structure and activity by kinetic capillary electrophoresis-MS.Nature chemical biology · 2016Article
- Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures.Journal of applied crystallography · 2016Article
- SAXS studies of RNA: structures, dynamics, and interactions with partners.Wiley interdisciplinary reviews. RNA · 2016Review
- Extracting water and ion distributions from solution x-ray scattering experiments.The Journal of chemical physics · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb(+) and Sr(2+)) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data at q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein-Zernike equations, with results from the Kovalenko-Hirata closure being closest to experiment for the cases studied here.
Indexed as
Identifiers
What OpenQuestion holds
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.