{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T14:21:39Z","timestamp":1781101299359,"version":"3.54.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Large-scale chemical cross-linking with mass spectrometry (XL-MS) analyses are quickly becoming a powerful means for high-throughput determination of protein structural information and protein\u2013protein interactions. Recent studies have garnered thousands of cross-linked interactions, yet the field lacks an effective tool to compile experimental data or access the network and structural knowledge for these large scale analyses. We present XLinkDB 2.0 which integrates tools for network analysis, Protein Databank queries, modeling of predicted protein structures and modeling of docked protein structures. The novel, integrated approach of XLinkDB 2.0 enables the holistic analysis of XL-MS protein interaction data without limitation to the cross-linker or analytical system used for the analysis.<\/jats:p>\n               <jats:p>Availability and Implementation: XLinkDB 2.0 can be found here, including documentation and help: http:\/\/xlinkdb.gs.washington.edu\/ .<\/jats:p>\n               <jats:p>Contact : jimbruce@uw.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw232","type":"journal-article","created":{"date-parts":[[2016,4,30]],"date-time":"2016-04-30T01:35:22Z","timestamp":1461980122000},"page":"2716-2718","source":"Crossref","is-referenced-by-count":64,"title":["XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data"],"prefix":"10.1093","volume":"32","author":[{"given":"Devin K.","family":"Schweppe","sequence":"first","affiliation":[{"name":"1 Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunxiang","family":"Zheng","sequence":"additional","affiliation":[{"name":"1 Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan D.","family":"Chavez","sequence":"additional","affiliation":[{"name":"1 Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arti T.","family":"Navare","sequence":"additional","affiliation":[{"name":"1 Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xia","family":"Wu","sequence":"additional","affiliation":[{"name":"1 Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jimmy K.","family":"Eng","sequence":"additional","affiliation":[{"name":"2 University of Washington Proteomics Resource, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James E.","family":"Bruce","sequence":"additional","affiliation":[{"name":"1 Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,4,29]]},"reference":[{"key":"2023020112590017500_btw232-B1","doi-asserted-by":"crossref","first-page":"7928","DOI":"10.1038\/ncomms8928","article-title":"Quantitative interactome analysis reveals a chemoresistant edgotype","volume":"6","author":"Chavez","year":"2015","journal-title":"Nat. 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Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/17\/2716\/49021457\/bioinformatics_32_17_2716.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/17\/2716\/49021457\/bioinformatics_32_17_2716.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:58:50Z","timestamp":1675292330000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/17\/2716\/2450733"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,4,29]]},"references-count":11,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2016,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw232","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,9,1]]},"published":{"date-parts":[[2016,4,29]]}}}