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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\u2013nucleic 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\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/gitlab.com\/topf-lab\/nucleospot\">https:\/\/gitlab.com\/topf-lab\/ProNA3D<\/jats:ext-link>\n                    . In addition, the repository contains the results of the large-scale analyses.\n                  <\/jats:p>","DOI":"10.34133\/csbj.0202","type":"journal-article","created":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T21:11:03Z","timestamp":1784841063000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark_01","source":"Crossref","is-referenced-by-count":0,"title":["ProNA3D: Distance-Based Analysis of Nucleic Acid-Containing Interfaces"],"prefix":"10.34133","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-7374-2525","authenticated-orcid":false,"given":"Luca R.","family":"Genz","sequence":"first","affiliation":[{"name":"Research Department of Integrative Virology, \rLeibniz-Institut f\u00fcr Virologie (LIV), Hamburg, Germany."},{"name":"Department of Chemistry, \rUniversit\u00e4t Hamburg, Hamburg, Germany."},{"name":"Centre for Structural Systems Biology (CSSB)","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8185-1215","authenticated-orcid":false,"given":"Maya","family":"Topf","sequence":"additional","affiliation":[{"name":"Research Department of Integrative Virology, \rLeibniz-Institut f\u00fcr Virologie (LIV), Hamburg, Germany."},{"name":"Centre for Structural Systems Biology (CSSB)","place":["Germany"]},{"name":"Institute for Molecular Virology and Tumorvirology, \rUniversit\u00e4tsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","published-online":{"date-parts":[[2026,9,14]]},"reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrm3884"},{"issue":"5","key":"e_1_3_4_3_2","doi-asserted-by":"crossref","first-page":"1223","DOI":"10.1093\/nar\/27.5.1223","article-title":"Conserved domains in DNA repair proteins and evolution of repair systems","volume":"27","author":"Aravind L","year":"1999","unstructured":"Aravind L, Walker DR, Koonin EV. 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