Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories

► Photon trajectories were measured for an ultrafast folding protein using single molecule FRET. ► Folding rates were obtained from a photon-by-photon analysis using a maximum likelihood method. ► Incorporating acceptor blinking into the analysis improved the accuracy of the extracted rates. ► The rates agree with the results from both the correlation analysis and ensemble laser temperature-jump.