KDSAXS: A Tool for Analyzing Binding Equilibria With SAXS Data Using Explicit Models

Abstract

KDSAXS is a computational tool for estimating dissociation constants (KD) from small-angle X-ray scattering (SAXS) titration experiments. By combining ensemble analysis with mass-balance equations, KDSAXS effectively models complex equilibria involving multiple species, ranging from simple oligomerization to transient and multivalent interactions, including intrinsically disordered proteins. For each species in equilibrium, the tool supports the integration of theoretical scattering profiles derived from ensemble structural models, X-ray crystallography, NMR, AlphaFold predictions, or molecular dynamics simulations. With its intuitive dashboard interface, KDSAXS enables researchers to input SAXS titration data, validate structural models and interactions, and compute species-specific scattering profiles. Additionally, it determines the relative populations of biomolecular species in equilibrium across user-defined Kᴅ ranges and concentrations. Applications of KDSAXS to systems such as beta-lactoglobulin oligomerization and the PCNA-p15PAF complex highlight its capacity to resolve complex equilibria and deliver accurate KD estimations. As an open-source platform, KDSAXS bridges computational and experimental methodologies, advancing SAXS-based analysis of macromolecular interactions and enhancing insights into dynamic biological systems. KDSAXS is freely accessible as a web server at https://kdsaxs.itqb.unl.pt.