ProNA3D

ProNA3D is a ChimeraX plug-in and command-line tool for analyzing nucleic acid-containing macromolecular complexes. It identifies interaction interfaces and spatially separated sub-interfaces in both experimental structures and computational models, including AlphaFold3 predictions. ProNA3D provides interactive 2D visualizations of interfaces, secondary-structure topology plots for RNA and DNA complexes, scoring metrics for predicted complexes, and options for detailed analysis of cryo-EM density maps.