{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T15:39:30Z","timestamp":1759160370566},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Chemical cross-linking with mass spectrometry (XL-MS) provides structural information for proteins and protein complexes in the form of crosslinked residue proximity and distance constraints between reactive residues. Utilizing spatial information derived from cross-linked residues can therefore assist with structural modeling of proteins. Selection of computationally derived model structures of proteins remains a major challenge in structural biology. The comparison of site interactions resulting from XL-MS with protein structure contact maps can assist the selection of structural models.<\/jats:p>\n               <jats:p>Availability and implementation: XLmap was implemented in R and is freely available at: http:\/\/brucelab.gs.washington.edu\/software.php.<\/jats:p>\n               <jats:p>Contact: \u00a0jimbruce@uw.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv519","type":"journal-article","created":{"date-parts":[[2015,9,27]],"date-time":"2015-09-27T23:57:20Z","timestamp":1443398240000},"page":"306-308","source":"Crossref","is-referenced-by-count":14,"title":["XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking"],"prefix":"10.1093","volume":"32","author":[{"given":"Devin K.","family":"Schweppe","sequence":"first","affiliation":[{"name":"Department of Genome Sciences, University of Washington, 850 Republican Ave, Seattle, WA 98109, USA"}]},{"given":"Juan D.","family":"Chavez","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, 850 Republican Ave, Seattle, WA 98109, USA"}]},{"given":"James E.","family":"Bruce","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, 850 Republican Ave, Seattle, WA 98109, USA"}]}],"member":"286","published-online":{"date-parts":[[2015,9,26]]},"reference":[{"key":"2023020110281478300_btv519-B1","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.ymeth.2015.05.014","article-title":"Protein structure prediction guided by crosslinking restraints\u2014a systematic evaluation of the impact of the crosslinking spacer length","volume":"89","author":"Hofmann","year":"2015","journal-title":"Methods"},{"key":"2023020110281478300_btv519-B2","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. 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