ArticleJournal of applied crystallography2024
Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications.
Article in Journal of applied crystallography, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- Phylogenetic Analysis and Structural Evaluation ofbioRxiv : the preprint server for biology · 2026Article
- Structure Characterization of Bacterial Microcompartment Shells via X-ray Scattering and Coordinate Modeling: Evidence for Adventitious Capture of Cytoplasmic Proteins.ACS applied bio materials · 2025Article
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2 authors.
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Abstract
X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclo-dextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software,
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