ArticleThe Journal of chemical physics2013
Fast-SAXS-pro: a unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes.
Article in The Journal of chemical physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 54 citations in OpenAlex.
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- A Novel Cell-Penetrating Lipopeptide for DNA Binding, Self-Assembly, and Delivery Into HeLa and Pluripotent Stem Cells.Journal of peptide science : an official publication of the European Peptide Society · 2026Article
- Small-angle X-ray scattering profile calculation for high-resolution models of biomacromolecules.Journal of applied crystallography · 2025Article
- Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.Nucleic acids research · 2024Article
- Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes.ArXiv · 2024Article
- Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations.Journal of chemical theory and computation · 2023Article
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Incorporation of DThe journal of physical chemistry. B · 2022Article
- A hybrid approach to study large conformational transitions of biomolecules from single particle XFEL diffraction data.Frontiers in molecular biosciences · 2022Article
- Combining Experimental Data and Computational Methods for the Non-Computer Specialist.Molecules (Basel, Switzerland) · 2020Review
- Protein Footprinting: Auxiliary Engine to Power the Structural Biology Revolution.Journal of molecular biology · 2020Review
- BEES: Bayesian Ensemble Estimation from SAS.Biophysical journal · 2019Article
- A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain.Structure (London, England : 1993) · 2019Article
- Article
- Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments.Biophysics and physicobiology · 2019Article
- Multidomain architecture of estrogen receptor reveals interfacial cross-talk between its DNA-binding and ligand-binding domains.Nature communications · 2018Article
- Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes.Angewandte Chemie (International ed. in English) · 2018Article
- Article
- Structures of Dynamic Protein Complexes: Hybrid Techniques to Study MAP Kinase Complexes and the ESCRT System.Methods in molecular biology (Clifton, N.J.) · 2018Article
- X-ray Scattering Studies of Protein Structural Dynamics.Chemical reviews · 2017Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
A generalized method, termed Fast-SAXS-pro, for computing small angle x-ray scattering (SAXS) profiles of proteins, nucleic acids, and their complexes is presented. First, effective coarse-grained structure factors of DNA nucleotides are derived using a simplified two-particle-per-nucleotide representation. Second, SAXS data of a 18-bp double-stranded DNA are measured and used for the calibration of the scattering contribution from excess electron density in the DNA solvation layer. Additional test on a 25-bp DNA duplex validates this SAXS computational method and suggests that DNA has a different contribution from its hydration surface to the total scattering compared to RNA and protein. To account for such a difference, a sigmoidal function is implemented for the treatment of non-uniform electron density across the surface of a protein/nucleic-acid complex. This treatment allows differential scattering from the solvation layer surrounding protein/nucleic-acid complexes. Finally, the applications of this Fast-SAXS-pro method are demonstrated for protein/DNA and protein/RNA complexes.
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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.