{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T03:27:26Z","timestamp":1773977246320,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Residue interaction networks (RINs) have been used in the literature to describe the protein 3D structure as a graph where nodes represent residues and edges physico\u2013chemical interactions, e.g. hydrogen bonds or van-der-Waals contacts. Topological network parameters can be calculated over RINs and have been correlated with various aspects of protein structure and function. Here we present a novel web server, RING, to construct physico\u2013chemically valid RINs interactively from PDB files for subsequent visualization in the Cytoscape platform. The additional structure-based parameters secondary structure, solvent accessibility and experimental uncertainty can be combined with information regarding residue conservation, mutual information and residue-based energy scoring functions. Different visualization styles are provided to facilitate visualization and standard plugins can be used to calculate topological parameters in Cytoscape. A sample use case analyzing the active site of glutathione peroxidase is presented.<\/jats:p>\n               <jats:p>Availability: The RING server, supplementary methods, examples and tutorials are available for non-commercial use at URL: http:\/\/protein.bio.unipd.it\/ring\/.<\/jats:p>\n               <jats:p>Contact: \u00a0silvio.tosatto@unipd.it<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr191","type":"journal-article","created":{"date-parts":[[2011,4,15]],"date-time":"2011-04-15T00:50:25Z","timestamp":1302828625000},"page":"2003-2005","source":"Crossref","is-referenced-by-count":122,"title":["RING: networking interacting residues, evolutionary information and energetics in protein structures"],"prefix":"10.1093","volume":"27","author":[{"given":"Alberto J. M.","family":"Martin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michele","family":"Vidotto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Filippo","family":"Boscariol","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom\u00e0s","family":"Di Domenico","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian","family":"Walsh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvio C. E.","family":"Tosatto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,4,14]]},"reference":[{"key":"2023012712455264800_B1","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1038\/35019019","article-title":"Error and attack tolerance of complex networks","volume":"406","author":"Albert","year":"2000","journal-title":"Nature"},{"key":"2023012712455264800_B2","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1093\/bioinformatics\/btm554","article-title":"Computing topological parameters of biological networks","volume":"24","author":"Assenov","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012712455264800_B3","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1126\/science.286.5439.509","article-title":"Emergence of scaling in random networks","volume":"286","author":"Barabasi","year":"1999","journal-title":"Science"},{"key":"2023012712455264800_B4","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1093\/bioinformatics\/btp135","article-title":"Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information","volume":"25","author":"Buslje","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012712455264800_B5","doi-asserted-by":"crossref","first-page":"e1000978","DOI":"10.1371\/journal.pcbi.1000978","article-title":"Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification","volume":"6","author":"Buslje","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"2023012712455264800_B6","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1016\/j.tibs.2008.09.006","article-title":"Creative elements: network-based predictions of active centres in proteins and cellular and social networks","volume":"33","author":"Csermely","year":"2008","journal-title":"Trends Biochem. Sci."},{"key":"2023012712455264800_B7","doi-asserted-by":"crossref","first-page":"R92","DOI":"10.1186\/gb-2007-8-5-r92","article-title":"Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages","volume":"8","author":"Del Sol","year":"2007","journal-title":"Genome Biol."},{"key":"2023012712455264800_B8","doi-asserted-by":"crossref","first-page":"8637","DOI":"10.1073\/pnas.122076099","article-title":"Topological determinants of protein folding","volume":"99","author":"Dokholyan","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012712455264800_B9","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023012712455264800_B10","doi-asserted-by":"crossref","first-page":"e9391","DOI":"10.1371\/journal.pone.0009391","article-title":"Atomic interaction networks in the core of protein domains and their native folds","volume":"5","author":"Soundararajan","year":"2010","journal-title":"PLoS One"},{"key":"2023012712455264800_B11","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nsb881","article-title":"Evolutionarily conserved networks of residues mediate allosteric communication in proteins","volume":"10","author":"Suel","year":"2003","journal-title":"Nat. Struct. Biol."},{"key":"2023012712455264800_B12","doi-asserted-by":"crossref","first-page":"10886","DOI":"10.1021\/bi049450k","article-title":"Using networks to identify fine structural differences between functionally distinct protein states","volume":"43","author":"Swint-Kruse","year":"2004","journal-title":"Biochemistry"},{"key":"2023012712455264800_B13","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1089\/ars.2008.2057","article-title":"Evolutionary and structural insights into the multifaceted glutathione peroxidase (Gpx) superfamily","volume":"10","author":"Toppo","year":"2008","journal-title":"Antioxid Redox Sign."},{"key":"2023012712455264800_B14","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.1089\/cmb.2005.12.1316","article-title":"The victor\/FRST function for model quality estimation","volume":"12","author":"Tosatto","year":"2005","journal-title":"J. Comput. Biol."},{"key":"2023012712455264800_B15","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1186\/1471-2105-8-155","article-title":"TAP score: torsion angle propensity normalization applied to local protein structure evaluation","volume":"8","author":"Tosatto","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012712455264800_B16","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.1089\/ars.2008.2055","article-title":"The catalytic site of glutathione peroxidases","volume":"10","author":"Tosatto","year":"2008","journal-title":"Antioxid Redox Sign."},{"key":"2023012712455264800_B17","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1038\/35054591","article-title":"Three key residues form a critical contact network in a protein folding transition state","volume":"409","author":"Vendruscolo","year":"2001","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/14\/2003\/48933298\/bioinformatics_27_14_2003.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/14\/2003\/48933298\/bioinformatics_27_14_2003.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:38:41Z","timestamp":1674826721000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/14\/2003\/193801"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,4,14]]},"references-count":17,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2011,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr191","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2011,7]]},"published":{"date-parts":[[2011,4,14]]}}}