{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T22:19:09Z","timestamp":1785536349949,"version":"3.56.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,4,20]],"date-time":"2023-04-20T00:00:00Z","timestamp":1681948800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 research and innovation program","award":["778247"],"award-info":[{"award-number":["778247"]}]},{"name":"European Union\u2019s Horizon 2020 research and innovation program","award":["823886"],"award-info":[{"award-number":["823886"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>\u2003<\/jats:title>\n                  <jats:p>RING-PyMOL is a plugin for PyMOL providing a set of analysis tools for structural ensembles and molecular dynamic simulations. RING-PyMOL combines residue interaction networks, as provided by the RING software, with structural clustering to enhance the analysis and visualization of the conformational complexity. It combines precise calculation of non-covalent interactions with the power of PyMOL to manipulate and visualize protein structures. The plugin identifies and highlights correlating contacts and interaction patterns that can explain structural allostery, active sites, and structural heterogeneity connected with molecular function. It is easy to use and extremely fast, processing and rendering hundreds of models and long trajectories in seconds. RING-PyMOL generates a number of interactive plots and output files for use with external tools. The underlying RING software has been improved extensively. It is 10 times faster, can process mmCIF files and it identifies typed interactions also for nucleic acids.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/BioComputingUP\/ring-pymol<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad260","type":"journal-article","created":{"date-parts":[[2023,4,20]],"date-time":"2023-04-20T18:32:15Z","timestamp":1682015535000},"source":"Crossref","is-referenced-by-count":34,"title":["RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics"],"prefix":"10.1093","volume":"39","author":[{"given":"Alessio","family":"Del Conte","sequence":"first","affiliation":[{"name":"Department of Biomedical Sciences, University of Padua , Padova 35121, 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 Information Engineering, University of Padua , Padova 35121, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damiano","family":"Clementel","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padua , Padova 35121, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giorgia F","family":"Camagni","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padua , Padova 35121, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7013-5785","authenticated-orcid":false,"given":"Giovanni","family":"Minervini","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padua , Padova 35121, 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 Padua , Padova 35121, 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 Padua , Padova 35121, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,4,20]]},"reference":[{"key":"2023050421470208500_btad260-B1","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkac365","article-title":"RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles","volume":"50","author":"Clementel","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023050421470208500_btad260-B2","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1093\/bib\/bbz029","article-title":"Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications","volume":"21","author":"Liang","year":"2020","journal-title":"Brief Bioinform"},{"key":"2023050421470208500_btad260-B3","doi-asserted-by":"crossref","first-page":"2003","DOI":"10.1093\/bioinformatics\/btr191","article-title":"RING: networking interacting residues, evolutionary information and energetics in protein structures","volume":"27","author":"Martin","year":"2011","journal-title":"Bioinformatics"},{"key":"2023050421470208500_btad260-B4","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkw315","article-title":"The RING 2.0 web server for high quality residue interaction networks","volume":"44","author":"Piovesan","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023050421470208500_btad260-B5","author":"Schr\u00f6dinger","year":"2015"},{"key":"2023050421470208500_btad260-B6","doi-asserted-by":"crossref","first-page":"e0255167","DOI":"10.1371\/journal.pone.0255167","article-title":"pyProGA\u2014a PyMOL plugin for protein residue network analysis","volume":"16","author":"Sladek","year":"2021","journal-title":"PLoS One"},{"key":"2023050421470208500_btad260-B7","doi-asserted-by":"crossref","DOI":"10.1038\/msb4100063","article-title":"Residues crucial for maintaining short paths in network communication mediate signaling in proteins","volume":"2","author":"del Sol","year":"2006","journal-title":"Mol Syst Biol"},{"key":"2023050421470208500_btad260-B8","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1021\/acs.jctc.1c00708","article-title":"PyLipID: a python package for analysis of protein\u2013lipid interactions from molecular dynamics simulations","volume":"18","author":"Song","year":"2022","journal-title":"J Chem Theory Comput"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad260\/50049335\/btad260.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/5\/btad260\/50204843\/btad260.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/5\/btad260\/50204843\/btad260.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T21:47:20Z","timestamp":1683236840000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad260\/7133739"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,4,20]]},"references-count":8,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2023,5,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad260","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,5,1]]},"published":{"date-parts":[[2023,4,20]]},"article-number":"btad260"}}