Pumilio-modified RNA interactions can be accurately predicted with λ-dynamics and Amber force fields. Comparison between λ-dynamics and in vitro ΔGbind measurements of human Pumilio 2 (hPUM2) binding to pseudouridine (Ψ) or N6-methyladenosine (m6A) modified RNA sequences performed previously (Vaidyanathan et al. 2017) or of binding data generated in this study (“PUM Library”). The experimental binding data (x-axis) are plotted against the extended 50 nsec λ-dynamics simulation results (y-axis) in kcal/mol. See Materials and Methods for details regarding the calculations performed. Shaded area, root mean square error (RMSE) of 1.0 kcal/mol. Error bars report the standard deviation from experimental sets. Mean unsigned errors (MUEs) and RMSEs reported for hPUM2 results computed with CHARMM36 (blue) and Amber (gold) force fields.
