{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T14:03:57Z","timestamp":1786025037476,"version":"3.56.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,3]],"date-time":"2016-10-03T00:00:00Z","timestamp":1475452800000},"content-version":"vor","delay-in-days":1941,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Chemical cross-linking of proteins or protein complexes and the mass spectrometry-based localization of the cross-linked amino acids in peptide sequences is a powerful method for generating distance restraints on the substrate's topology.<\/jats:p>\n               <jats:p>Results: Here, we introduce the algorithm Xwalk for predicting and validating these cross-links on existing protein structures. Xwalk calculates and displays non-linear distances between chemically cross-linked amino acids on protein surfaces, while mimicking the flexibility and non-linearity of cross-linker molecules. It returns a \u2018solvent accessible surface distance\u2019, which corresponds to the length of the shortest path between two amino acids, where the path leads through solvent occupied space without penetrating the protein surface.<\/jats:p>\n               <jats:p>Availability: Xwalk is freely available as a web server or stand-alone JAVA application at http:\/\/www.xwalk.org.<\/jats:p>\n               <jats:p>Contact: \u00a0abdullah@imsb.biol.ethz.ch; aebersold@imsb.biol.ethz.ch<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr348","type":"journal-article","created":{"date-parts":[[2011,6,12]],"date-time":"2011-06-12T00:35:05Z","timestamp":1307838905000},"page":"2163-2164","source":"Crossref","is-referenced-by-count":156,"title":["Xwalk: computing and visualizing distances in cross-linking experiments"],"prefix":"10.1093","volume":"27","author":[{"given":"Abdullah","family":"Kahraman","sequence":"first","affiliation":[{"name":"Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH Zurich), CH-8093 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars","family":"Malmstr\u00f6m","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH Zurich), CH-8093 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruedi","family":"Aebersold","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH Zurich), CH-8093 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,6,11]]},"reference":[{"key":"2023012511545155800_B1","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1002\/prot.22633","article-title":"On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins","volume":"78","author":"Kahraman","year":"2010","journal-title":"Proteins"},{"key":"2023012511545155800_B2","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1016\/j.jmb.2007.11.035","article-title":"Molecular model of an alpha-helical prion protein dimer and its monomeric subunits as derived from chemical cross-linking and molecular modeling calculations","volume":"376","author":"Kaimann","year":"2008","journal-title":"J. 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Biocomput."},{"key":"2023012511545155800_B8","doi-asserted-by":"crossref","first-page":"13711","DOI":"10.1021\/bi701042e","article-title":"Intramolecular cross-linking evaluated as a structural probe of the protein folding transition state","volume":"46","author":"Shandiz","year":"2007","journal-title":"Biochemistry"},{"key":"2023012511545155800_B9","doi-asserted-by":"crossref","first-page":"3583","DOI":"10.1021\/pr1001115","article-title":"Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: a novel method to determine interresidue distances in protein structures through cross-linking","volume":"9","author":"Zelter","year":"2010","journal-title":"J. Proteome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/15\/2163\/48865208\/bioinformatics_27_15_2163.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/15\/2163\/48865208\/bioinformatics_27_15_2163.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T12:06:11Z","timestamp":1674648371000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/15\/2163\/404176"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,6,11]]},"references-count":9,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2011,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr348","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,8,1]]},"published":{"date-parts":[[2011,6,11]]}}}