ProNA3D: Distance-Based Analysis of Nucleic Acid-Containing Interfaces

Biomolecular interactions are central to many essential cellular processes, but RNA-containing complexes remain challenging to resolve structurally, even as experimental methods and AI-based prediction have expanded structural coverage. Tools for the integrated analysis of interfaces within such complexes remain limited. We present ProNA3D, a tool that provides a unified platform for analyzing protein-nucleic acid and nucleic acid-only complexes, bridging the gap between structure prediction and functional interpretation. ProNA3D supports both experimental and computationally predicted structures, incorporating scoring metrics for AlphaFold 3 predictions. It also offers interactive 2-dimensional interface visualization and secondary-structure topology plots for RNA and DNA. An interface-based density zoning feature facilitates structure analysis of cryo-electron microscopy maps, allowing the evaluation of dynamic complexes in the context of heterogeneous density. We demonstrate ProNA3D on diverse complexes solved by x-ray crystallography or cryo-electron microscopy, as well as on computational models. In one example, ProNA3D identified a high-connectivity nucleotide with potential functional relevance in a trimeric complex of HIV-1 RNA and a human antibody. Applying ProNA3D to the entire Protein Data Bank revealed distinct interface connectivity trends and interaction modes characteristic of specific classes of nucleic acid-containing complexes (e.g., methyltransferase-DNA and CRISPR-associated). The method is available as both a UCSF ChimeraX plug-in for visualization and a command-line tool at https://gitlab.com/topf-lab/ProNA3D. In addition, the repository contains the results of the large-scale analyses.