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Thanks to the advances in network theory, RINs have been proved effective as an alternative to coordinate data in the analysis of complex systems. The RING server calculates high quality and reliable non-covalent molecular interactions based on geometrical parameters. Here, we present the new RING 3.0 version extending the previous functionality in several ways. The underlying software library has been re-engineered to improve speed by an order of magnitude. RING now also supports the mmCIF format and provides typed interactions for the entire PDB chemical component dictionary, including nucleic acids. Moreover, RING now employs probabilistic graphs, where multiple conformations (e.g. NMR or molecular dynamics ensembles) are mapped as weighted edges, opening up new ways to analyze structural data. The web interface has been expanded to include a simultaneous view of the RIN alongside a structure viewer, with both synchronized and clickable. Contact evolution across models (or time) is displayed as a heatmap and can help in the discovery of correlating interaction patterns. The web server, together with an extensive help and tutorial, is available from URL: https:\/\/ring.biocomputingup.it\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac365","type":"journal-article","created":{"date-parts":[[2022,4,30]],"date-time":"2022-04-30T19:09:19Z","timestamp":1651345759000},"page":"W651-W656","source":"Crossref","is-referenced-by-count":178,"title":["RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles"],"prefix":"10.1093","volume":"50","author":[{"given":"Damiano","family":"Clementel","sequence":"first","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova\u00a035131, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessio","family":"Del\u00a0Conte","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova\u00a035131, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0362-8218","authenticated-orcid":false,"given":"Alexander Miguel","family":"Monzon","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova\u00a035131, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giorgia\u00a0F","family":"Camagni","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova\u00a035131, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanni","family":"Minervini","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova\u00a035131, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8210-2390","authenticated-orcid":false,"given":"Damiano","family":"Piovesan","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova\u00a035131, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4525-7793","authenticated-orcid":false,"given":"Silvio C E","family":"Tosatto","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova\u00a035131, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,5,12]]},"reference":[{"key":"2022070423575135300_B1","doi-asserted-by":"crossref","first-page":"1042","DOI":"10.1126\/science.1219021","article-title":"The protein-folding problem, 50 years on","volume":"338","author":"Dill","year":"2012","journal-title":"Science"},{"key":"2022070423575135300_B2","doi-asserted-by":"crossref","first-page":"2006.0019","DOI":"10.1038\/msb4100063","article-title":"Residues crucial for maintaining short paths in network communication mediate signaling in proteins","volume":"2","author":"del\u00a0Sol","year":"2006","journal-title":"Mol. 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