SAXS Assistant: Automated SAXS analysis for structural discovery in biologics and polymeric nanoparticles

Journal Article · Wed Sep 24 00:00:00 EDT 2025 · Biophysical Journal

DOI:https://doi.org/10.1016/j.bpj.2025.09.034· OSTI ID:3010731

Ramirez, Cesar ^[1]; Di Mare, Elena ^[1]; Byrnes, James ^[2]; Ahmed, Eman ^[1]; Pineiro-Goncalves, Maria ^[1]; Lopez, Cristian ^[1]; Murthy, N. Sanjeeva ^[1]; Gormley, Adam J. ^[1]

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1. Rutgers Univ., Piscataway, NJ (United States)
2. Brookhaven National Laboratory (BNL), Upton, NY (United States). National Synchrotron Light Source II (NSLS-II)

Small-angle x-ray scattering (SAXS) is a powerful technique for assessing macromolecular structure. High-throughput SAXS is limited by the time-consuming and, at times, subjective nature of SAXS data interpretation. Here, we present SAXS Assistant, a Python-based script that streamlines SAXS data analysis to extract features for machine learning (ML) and key structural parameters, including the Guinier radius of gyration (R_g), pair distance distribution function (PDDF)-derived R_g, maximum particle dimension (D_max), and Kratky plots. The script builds upon BioXTAS RAW and validates reliability via Guinier/PDDF R_g agreement, an important indicator of well-measured data sets. For assistance in D_max estimation, a multilayer perceptron regressor was trained with 1940 data files from the Small Angle Scattering Biological Data Bank. The model achieved a test set performance R² = 0.90 and mean absolute error = 11.7 Å. Training exclusively with experimental data translates analyses from researchers, including experts in the field, to the ML model, which helps assess D_max estimations from PDDF. Gaussian mixture model clustering was implemented to classify profiles into structural classes based on entries in the Small Angle Scattering Biological Data Bank. Users may therefore assess the similarity between experimental samples and known biomolecular shapes within the mapped repository entries. This probabilistic clustering aids in quantifying information from Kratky and generating shape-descriptive features. SAXS Assistant accelerates SAXS data analysis through enforced quality control, ML-ready outputs, and flags for low-confidence results. In addition to providing the ability to analyze large data sets at high throughput, this tool is versatile and may serve researchers in both biological and synthetic polymer research fields.

• Research Organization: Brookhaven National Laboratory (BNL), Upton, NY (United States)
• Sponsoring Organization: National Institutes of Health (NIH); National Science Foundation (NSF); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: SC0012704
• OSTI ID: 3010731
• Report Number(s): BNL--229267-2025-JAAM
• Journal Information: Biophysical Journal, Journal Name: Biophysical Journal Journal Issue: 21 Vol. 124; ISSN 0006-3495
• Publisher: Elsevier
• Country of Publication: United States
• Language: English

Related Subjects

36 MATERIALS SCIENCE
high-throughput analysis
intrinsically disordered protein
machine learning