Extended Data Fig. 10: RRE structure calculation from experimental AFM data using HORNET and conformational heterogeneity.
From: Determining structures of RNA conformers using AFM and deep neural networks
a, Surface plot, showing the population density as a function of total energy and goodness-of-fit to the AFM molecular surface (CC), for the trajectory models from each of the five selected RRE conformers from left to right: C0, C1, C2, C3, and C4. The star symbols represent the top-20 scored models, based on estimated RMSD. b, AFM image of HIV-1 RRE RNA. c, AFM image of the RRE RNA in the presence of peptide. d, AFM tally of the surface area using the raw image of RRE in the absence (red) or presence (blue) of the peptide. The RRE shows a more homogenous conformational distribution in the presence of the peptide. The raw images in b and c were taken once thus without signal-averaging.
