Use of single-molecule time-series data for refining conformational dynamics in molecular simulations

•Experimental measurements integrated with molecular dynamics simulations to understand structure–dynamics–function relationships.•Molecular simulations utilized to refine the quality of ensemble measurements in NMR, SAXS, or cryo-EM.•Model-free analysis applied to single-molecule time-series data through statistical analysis methods.•Markov State models linking MD simulations and experimental time-series data for describing conformational dynamics of biomolecules. Atomically detailed description of conformational dynamics in biomolecules is often essential to understand biological functions. Combining experimental measurements with molecular simulations significantly improves the outcome. Ensemble refinements, where the simulations are utilized to refine ensemble averaged data in NMR, SAXS, or cryo-EM, are a popular approach in integrative structural biology. Single-molecule time-series data contain rich temporal information of biomolecular dynamics. However, direct usage of the time-series data together with molecular simulations is just beginning. Here, we review data-assimilation approaches linking molecular simulations with experimental time-series data and discuss current limitations and potential applications of this approach in integrative structural biology.