{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,8,8]],"date-time":"2023-08-08T19:14:08Z","timestamp":1691522048267},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,1]]},"abstract":"Abstract<\/jats:title>\n Summary: We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology.<\/jats:p>\n Availability and implementation: The Protein Topology Graph Library server is freely available on the web at http:\/\/ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http:\/\/vplg.sourceforge.net.<\/jats:p>\n Contact: \u00a0tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv574","type":"journal-article","created":{"date-parts":[[2015,10,8]],"date-time":"2015-10-08T01:29:10Z","timestamp":1444267750000},"page":"474-476","source":"Crossref","is-referenced-by-count":6,"title":["The new protein topology graph library web server"],"prefix":"10.1093","volume":"32","author":[{"given":"Tim","family":"Sch\u00e4fer","sequence":"first","affiliation":[{"name":"1 Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany and"}]},{"given":"Andreas","family":"Scheck","sequence":"additional","affiliation":[{"name":"1 Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany and"}]},{"given":"Daniel","family":"Brune\u00df","sequence":"additional","affiliation":[{"name":"1 Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany and"}]},{"given":"Patrick","family":"May","sequence":"additional","affiliation":[{"name":"2 Genome Analysis, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg"}]},{"given":"Ina","family":"Koch","sequence":"additional","affiliation":[{"name":"1 Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany and"}]}],"member":"286","published-online":{"date-parts":[[2015,10,6]]},"reference":[{"key":"2023020110312923800_btv574-B1","doi-asserted-by":"crossref","first-page":"D419","DOI":"10.1093\/nar\/gkm993","article-title":"Data growth and its impact on the SCOP database: new developments","volume":"36","author":"Andreeva","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023020110312923800_btv574-B2","first-page":"361","article-title":"Gephi: an open source software for exploring and manipulating networks","author":"Bastian","year":"2009"},{"key":"2023020110312923800_btv574-B3","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023020110312923800_btv574-B4","doi-asserted-by":"crossref","first-page":"2366","DOI":"10.1038\/nprot.2007.324","article-title":"Integration of biological networks and gene expression data using cytoscape","volume":"2","author":"Cline","year":"2007","journal-title":"Nat. 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