From quantitative modeling of fluorescence experiments on biomolecules to the prediction of spectroscopic dye properties

Abstract

Fluorescence spectroscopy and modeling provide powerful means to characterize biomacromolecular structures, dynamics, and interactions. F\"orster resonance energy transfer serves as a key technique for this due to its nanometer-scale distance sensitivity. Quantitative interpretation of fluorescence data relies on models that link molecular structure to observable spectroscopic quantities and vice versa. Integrative modelling frameworks combine fluorescence observables with complementary structural information to infer molecular structures and conformational ensembles. This review outlines conceptual components of fluorescence-based modeling, discusses dye representations, and highlights advances toward refined models enabling quantitative structural analysis. Finally, we discuss the prediction of spectroscopic properties of dyes based on biomolecular structures and fluorescence assay design beyond traditional FRET applications.