ArticleJournal of applied crystallography2009
SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules.
Article in Journal of applied crystallography, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Small-angle X-ray scattering profile calculation for high-resolution models of biomacromolecules.Journal of applied crystallography · 2025Article
- Fitting high-resolution electron density maps from atomic models to solution scattering data.Biophysical journal · 2023Article
- Real-time tracking of protein unfolding with time-resolved x-ray solution scattering.Structural dynamics (Melville, N.Y.) · 2020Article
- Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering.IUCrJ · 2020Article
- Article
- Predicting X-ray solution scattering from flexible macromolecules.Protein science : a publication of the Protein Society · 2018Article
- X-ray Scattering Studies of Protein Structural Dynamics.Chemical reviews · 2017Review
- Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations.The Journal of chemical physics · 2016Article
- SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell.Biophysical journal · 2016Article
- Modulation of HIV protease flexibility by the T80N mutation.Proteins · 2015Article
- Interpretation of solution x-ray scattering by explicit-solvent molecular dynamics.Biophysical journal · 2015Article
- Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.Nano reviews · 2015Article
- Uniqueness of models from small-angle scattering data: the impact of a hydration shell and complementary NMR restraints.Acta crystallographica. Section D, Biological crystallography · 2015Article
- Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids.The Journal of chemical physics · 2014Article
- Methods for SAXS-based structure determination of biomolecular complexes.Advanced materials (Deerfield Beach, Fla.) · 2014Article
- MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins.Journal of applied crystallography · 2014Article
- Validating solution ensembles from molecular dynamics simulation by wide-angle X-ray scattering data.Biophysical journal · 2014Article
- HierarchicalJournal of applied crystallography · 2014Article
- Accurate SAXS profile computation and its assessment by contrast variation experiments.Biophysical journal · 2013Article
- A hierarchical algorithm for fast Debye summation with applications to small angle scattering.Journal of computational chemistry · 2012Article
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Authors and funding
3 authors.
Funding
Abstract
This paper describes a computational approach to estimating wide-angle X-ray solution scattering (WAXS) from proteins, which has been implemented in a computer program called SoftWAXS. The accuracy and efficiency of SoftWAXS are analyzed for analytically solvable model problems as well as for proteins. Key features of the approach include a numerical procedure for performing the required spherical averaging and explicit representation of the solute-solvent boundary and the surface of the hydration layer. These features allow the Fourier transform of the excluded volume and hydration layer to be computed directly and with high accuracy. This approach will allow future investigation of different treatments of the electron density in the hydration shell. Numerical results illustrate the differences between this approach to modeling the excluded volume and a widely used model that treats the excluded-volume function as a sum of Gaussians representing the individual atomic excluded volumes. Comparison of the results obtained here with those from explicit-solvent molecular dynamics clarifies shortcomings inherent to the representation of solvent as a time-averaged electron-density profile. In addition, an assessment is made of how the calculated scattering patterns depend on input parameters such as the solute-atom radii, the width of the hydration shell and the hydration-layer contrast. These results suggest that obtaining predictive calculations of high-resolution WAXS patterns may require sophisticated treatments of solvent.
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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.